Ndufb1 (MNLL) is one of the smallest accessory subunits of mitochondrial NADH:ubiquinone oxidoreductase (Complex I), a 45-subunit enzyme of the inner mitochondrial membrane that transfers electrons from NADH to ubiquinone and couples this to proton translocation. The 57-amino-acid protein contains a single transmembrane helix that anchors it in the membrane arm near the core subunit ND4, with a short C-terminal domain exposed to the mitochondrial matrix. As a non-catalytic accessory subunit, Ndufb1 contributes to the structural integrity of Complex I and is incorporated during the ND4-module stage of the modular assembly pathway. Cryo-EM structures from mouse heart mitochondria confirm its position in the membrane domain, where it contacts neighboring beta-subcomplex subunits NDUFB4, NDUFB5, NDUFB8, and NDUFB11.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0045271
respiratory chain complex I
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Phylogenetic inference that Ndufb1 is part of respiratory chain complex I. Consistent with all structural and biochemical evidence showing NDUFB1 as an integral subunit of Complex I across eukaryotes.
Supporting Evidence:
PMID:38575788
Supercomplexes of the respiratory chain...mammalian (mouse) tissues contain three defined types of 'respirasome', supercomplexes made of CI, CIII2 and CIV
|
|
GO:0005739
mitochondrion
|
IEA
GO_REF:0000120 |
KEEP AS NON CORE |
Summary: Automated annotation placing Ndufb1 in the mitochondrion. Correct but less specific than the mitochondrial inner membrane annotation which is also present. Subsumed by the more specific localization.
Supporting Evidence:
PMID:38575788
Supercomplexes of the respiratory chain...mammalian (mouse) tissues contain three defined types of 'respirasome'
|
|
GO:0005743
mitochondrial inner membrane
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Automated annotation for mitochondrial inner membrane localization. Correct and supported by direct structural evidence from cryo-EM of mouse Complex I showing NDUFB1 embedded in the inner membrane with a single transmembrane helix.
Supporting Evidence:
PMID:38575788
Supercomplexes of the respiratory chain...mammalian (mouse) tissues contain three defined types of 'respirasome', supercomplexes made of CI, CIII2 and CIV
|
|
GO:0045271
respiratory chain complex I
|
IEA
GO_REF:0000107 |
ACCEPT |
Summary: Ensembl Compara-based transfer from human ortholog. Correct and redundant with the IBA and IDA annotations for the same term.
Supporting Evidence:
PMID:38575788
Supercomplexes of the respiratory chain...mammalian (mouse) tissues contain three defined types of 'respirasome', supercomplexes made of CI, CIII2 and CIV
|
|
GO:0005739
mitochondrion
|
ISO
GO_REF:0000119 |
KEEP AS NON CORE |
Summary: Manual transfer from human ortholog O75438. Correct but less specific than the inner membrane annotation.
Supporting Evidence:
PMID:38575788
Supercomplexes of the respiratory chain...mammalian (mouse) tissues contain three defined types of 'respirasome'
|
|
GO:0005743
mitochondrial inner membrane
|
ISO
GO_REF:0000119 |
ACCEPT |
Summary: Manual transfer from human ortholog O75438 for mitochondrial inner membrane localization. Correct, and confirmed directly in mouse by cryo-EM (PMID:38575788).
Supporting Evidence:
PMID:38575788
Supercomplexes of the respiratory chain...mammalian (mouse) tissues contain three defined types of 'respirasome', supercomplexes made of CI, CIII2 and CIV
|
|
GO:0045271
respiratory chain complex I
|
ISO
GO_REF:0000119 |
ACCEPT |
Summary: Manual transfer from human ortholog. Correct and redundant with IDA and IBA annotations for the same term.
Supporting Evidence:
PMID:38575788
Supercomplexes of the respiratory chain...mammalian (mouse) tissues contain three defined types of 'respirasome', supercomplexes made of CI, CIII2 and CIV
|
|
GO:0016607
nuclear speck
|
ISO
GO_REF:0000119 |
MARK AS OVER ANNOTATED |
Summary: Transfer from human ortholog O75438 for nuclear speck localization. This is a questionable annotation for a well-characterized mitochondrial inner membrane protein. NDUFB1 is a single-pass transmembrane protein that is an integral part of the membrane arm of Complex I. No published study has demonstrated dual mitochondrial/nuclear localization for this protein. The human annotation may derive from a high-throughput study with false-positive nuclear detections, possibly due to the very small size of the protein (57 aa) leading to mislocalization artifacts.
Reason: No credible evidence supports nuclear speck localization for a small transmembrane Complex I subunit. Likely a false positive from high-throughput localization screening.
|
|
GO:0009060
aerobic respiration
|
NAS
PMID:30030361 Assembly of mammalian oxidative phosphorylation complexes I-... |
KEEP AS NON CORE |
Summary: ComplexPortal annotation based on the review by Signes and Fernandez-Vizarra 2018. As a structural subunit of Complex I, NDUFB1 participates in the respiratory chain and therefore in aerobic respiration. The term is correct but broad; the more specific process is mitochondrial electron transport from NADH to ubiquinone.
Supporting Evidence:
PMID:30030361
The assembly of the five oxidative phosphorylation system (OXPHOS) complexes in the inner mitochondrial membrane is an intricate process
|
|
GO:0042776
proton motive force-driven mitochondrial ATP synthesis
|
NAS
PMID:30030361 Assembly of mammalian oxidative phosphorylation complexes I-... |
KEEP AS NON CORE |
Summary: ComplexPortal annotation. Complex I contributes to the proton motive force by pumping protons across the inner membrane, which drives ATP synthase. NDUFB1 as a structural subunit contributes indirectly to this process. However, NDUFB1 itself is not in the proton-pumping modules directly; it is a structural element. The annotation is not wrong but represents an indirect contribution.
Supporting Evidence:
PMID:30030361
The assembly of the five oxidative phosphorylation system (OXPHOS) complexes in the inner mitochondrial membrane is an intricate process
|
|
GO:0005743
mitochondrial inner membrane
|
IDA
PMID:38575788 SCAF1 drives the compositional diversity of mammalian respir... |
ACCEPT |
Summary: Direct experimental evidence from cryo-EM of mouse heart mitochondria showing NDUFB1 as part of Complex I in the inner membrane. The is_active_in qualifier is appropriate since this is where the protein functions as part of the respirasome.
Supporting Evidence:
PMID:38575788
mammalian (mouse) tissues contain three defined types of 'respirasome', supercomplexes made of CI, CIII2 and CIV
|
|
GO:0045271
respiratory chain complex I
|
IDA
PMID:38575788 SCAF1 drives the compositional diversity of mammalian respir... |
ACCEPT |
Summary: Direct experimental evidence from cryo-EM structures of mouse respirasomes. Ndufb1 is resolved as chain f in the Complex I structure. This is the strongest evidence for this annotation.
Supporting Evidence:
PMID:38575788
mammalian (mouse) tissues contain three defined types of 'respirasome', supercomplexes made of CI, CIII2 and CIV
|
|
GO:0045271
respiratory chain complex I
|
ISS
GO_REF:0000024 |
ACCEPT |
Summary: Manual sequence similarity-based transfer. Correct and consistent with direct experimental evidence from mouse cryo-EM studies.
Supporting Evidence:
PMID:38575788
mammalian (mouse) tissues contain three defined types of 'respirasome', supercomplexes made of CI, CIII2 and CIV
|
|
GO:0005198
structural molecule activity
|
ISS | NEW |
Summary: NDUFB1 is a non-catalytic accessory subunit of Complex I. It lacks any catalytic motifs and its role is structural: stabilizing the membrane arm of Complex I around the ND4 core subunit. Structural molecule activity is the appropriate molecular function for accessory subunits that contribute to complex integrity without independent enzymatic activity.
Reason: No molecular function annotation currently exists for Ndufb1. As a non-catalytic accessory subunit, structural molecule activity is the most appropriate MF term.
Supporting Evidence:
PMID:38575788
mammalian (mouse) tissues contain three defined types of 'respirasome', supercomplexes made of CI, CIII2 and CIV
PMID:27626371
Complex I (NADH:ubiquinone oxidoreductase) is the first enzyme of the mitochondrial respiratory chain and is composed of 45 subunits in humans
file:mouse/Ndufb1/Ndufb1-deep-research-bioreason-sft.md
A small, non-catalytic accessory subunit tailored to the membrane arm of respiratory complex I...This architecture causes the protein to function as a structural and organizational element rather than as an active redox catalyst
|
|
GO:0032981
mitochondrial respiratory chain complex I assembly
|
ISS | NEW |
Summary: NDUFB1 is incorporated during the ND4-module stage of Complex I assembly. Systematic studies of accessory subunits in human cells (PMID:27626371) demonstrate that loss of accessory subunits disrupts Complex I assembly. NDUFB1 is part of the ND4-module assembly intermediate along with NDUFB4, NDUFB5, NDUFB6, NDUFB10, NDUFB11.
Reason: No Complex I assembly annotation is present despite evidence that NDUFB1 is part of a defined assembly intermediate (ND4-module).
Supporting Evidence:
PMID:27626371
Complex I (NADH:ubiquinone oxidoreductase) is the first enzyme of the mitochondrial respiratory chain and is composed of 45 subunits in humans
PMID:30030361
The human enzymes comprise core proteins, performing the catalytic activities, and a large number of 'supernumerary' subunits that play essential roles in assembly, regulation and stability
|
|
GO:0006120
mitochondrial electron transport, NADH to ubiquinone
|
NAS
PMID:30030361 Assembly of mammalian oxidative phosphorylation complexes I-... |
NEW |
Summary: As a structural subunit of Complex I, NDUFB1 is essential for the complex-level activity of NADH to ubiquinone electron transfer. Although NDUFB1 itself is non-catalytic, loss of accessory subunits abolishes Complex I activity. This is more specific than the existing aerobic respiration annotation.
Reason: This process term more precisely describes the role of Complex I in mitochondrial electron transport than the broader aerobic respiration term already present.
Supporting Evidence:
PMID:30030361
The assembly of the five oxidative phosphorylation system (OXPHOS) complexes in the inner mitochondrial membrane is an intricate process
PMID:38575788
mammalian (mouse) tissues contain three defined types of 'respirasome', supercomplexes made of CI, CIII2 and CIV
|
Q: What is the specific phenotype of Ndufb1 knockout in mouse cells or tissues? Does loss of NDUFB1 lead to complete loss of Complex I, or is a partially assembled complex retained?
Suggested experts: Stroud DA
Q: Does NDUFB1 have any role in stabilizing respiratory supercomplexes (respirasomes) beyond its role within Complex I itself?
Suggested experts: Sazanov LA, Vercellino I
Experiment: CRISPR knockout of Ndufb1 in mouse cell lines followed by complexome profiling to determine whether loss of NDUFB1 specifically disrupts the ND4-module assembly intermediate or affects broader Complex I stability.
Type: complexome profiling
Experiment: Crosslinking mass spectrometry of purified mouse Complex I to map the direct protein-protein contacts of NDUFB1 and determine whether it bridges the ND4-module to adjacent assembly modules.
Type: XL-MS
---
provider: bioreason-pro
model: SFT
source: huggingface.co/datasets/wanglab/protein_catalogue
date: '2026-04-04'
uniprot_id: P0DN34
gene: Ndufb1
organism: Mus musculus (Mouse)
---
## Thinking Trace
I begin with the InterPro architecture: IPR012575 (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 family) spans residues 1–57, covering essentially the entire polypeptide. A single, compact family domain of this length indicates a small, non-catalytic accessory subunit tailored to the membrane arm of respiratory complex I. NDUB1-family proteins are typically single-pass inner-membrane proteins with a short matrix-exposed region that dock onto neighboring transmembrane subunits. This architecture causes the protein to function as a structural and organizational element rather than as an active redox catalyst.
From this domain assignment and topology, the molecular function is best understood as participation in the enzymatic activity of complex I. Although the polypeptide lacks catalytic motifs, its embedding within the membrane arm positions it to stabilize the quinone-reactive module and to maintain the geometry required for electron transfer from NADH to ubiquinone. In GO terms, this supports the complex-level function formalized as GO:0008137 NADH dehydrogenase (ubiquinone) activity, with the caveat that the subunit itself is non-enzymatic and contributes structurally to that activity.
The biological process follows from the assembly logic of the respiratory chain. Accessory membrane subunits of the beta subcomplex (including NDUB1) nucleate and stabilize late-stage intermediates of complex I, ensuring proper incorporation of acyl carrier protein and other small membrane components. This assembly role provides a mechanistic route to influence the maturation and stability of the entire oxidative phosphorylation machinery. Through these assembly-dependent effects and potential transient contacts at supercomplex interfaces, the protein can contribute to GO:0034551 mitochondrial respiratory chain complex III assembly, helping coordinate the integrity of the III–I neighborhood that supports efficient electron flow.
Cellular localization is dictated by the single-pass membrane architecture and the NDUB1 family signature. The protein integrates into the mitochondrial inner membrane as a matrix-side peripheral element, consistent with a single transmembrane helix anchoring a matrix-exposed domain that contacts neighboring subunits. This places it within the GO:0005739 mitochondrion and more specifically at the inner membrane, where complex I resides.
A mechanistic hypothesis emerges from the interaction landscape. Contacts with NDUFB11, NDUFB5, NDUFB10, and NDUFB4 indicate lateral packing within the beta subcomplex; associations with NDUFA1, NDUFA2, NDUFA6, NDUFA8, and C2 (a core membrane anchor) position the subunit at a junction between the peripheral and membrane arms, where it can brace the quinone-access channel. Binding to the mitochondrial acyl carrier protein suggests a role in stabilizing the ACP module that is essential for complex I maturation. By organizing these interfaces, the subunit preserves the conformational coupling that allows electron transfer from NADH to be transmitted into controlled conformational changes that drive proton translocation across the inner membrane, thereby sustaining oxidative phosphorylation.
## Functional Summary
A small, single-pass inner-membrane accessory subunit of mitochondrial complex I that anchors on the matrix side to stabilize the membrane arm and organize neighboring subunits around the quinone-reactive region. By scaffolding assembly intermediates and maintaining the geometry of the electron-transfer module, it supports the transfer of electrons from NADH to ubiquinone and couples this chemistry to proton pumping, thereby sustaining oxidative phosphorylation. Its assembly-stabilizing role likely extends to the integrity of adjacent respiratory supercomplexes.
## UniProt Summary
Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. Essential for the catalytic activity of complex I. Essential for oxidative phosphorylation.
## InterPro Domains
- IPR012575: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 (family) [1-57]
## GO Term Predictions
### Molecular Function
### Biological Process
### Cellular Component
Ndufb1 encodes a small, single-pass transmembrane accessory subunit of mitochondrial NADH:ubiquinone oxidoreductase (Complex I). The protein has a transmembrane helix (residues 10-26) and a C-terminal matrix-exposed domain. It is one of the smallest subunits of Complex I and belongs to the NDUFB1/MNLL family (InterPro: IPR012575, Pfam: PF08040).
"SCAF1 drives the compositional diversity of mammalian respirasomes."
- Cryo-EM structures of mouse mitochondrial supercomplexes at 3.6 A resolution
- Directly demonstrates Ndufb1 as part of Complex I in mouse tissue (heart mitochondria)
- Confirms subcellular location: mitochondrial inner membrane, matrix side
- Confirms subunit composition of Complex I (45 subunits)
- This is the primary IDA evidence for the mouse protein
"Assembly of mammalian oxidative phosphorylation complexes I-V and supercomplexes."
- Review article covering assembly pathways of all five OXPHOS complexes
- Describes Complex I assembly as modular, with NDUFB1 being part of the ND4-module
- Cited by ComplexPortal for NAS annotations on aerobic respiration and proton motive force-driven ATP synthesis
- REAL reference, verified
"Lineage-specific biology revealed by a finished genome assembly of the mouse."
- Mouse genome assembly paper (C57BL/6J strain)
- Provides the genomic sequence for Ndufb1
- Not directly relevant to protein function
"Accessory subunits are integral for assembly and function of human mitochondrial complex I."
- Systematic CRISPR knockout study of all 31 accessory subunits in human cells
- NDUFB1 knockout was included; loss of accessory subunits generally leads to loss of Complex I activity
- Demonstrates that accessory subunits are essential for assembly and function
"The assembly pathway of mitochondrial respiratory chain complex I."
- Dynamic complexome profiling of Complex I assembly
- NDUFB1 is part of the ND4-module assembly intermediate along with NDUFB4, NDUFB5, NDUFB6, NDUFB10, NDUFB11
The BioReason deep research file makes several claims that need verification:
INCORRECT: This is Complex III assembly, not Complex I. NDUFB1 is a Complex I subunit with no known role in Complex III assembly. The BioReason model appears to have confused "integrity of the III-I neighborhood" (supercomplex interactions) with Complex III assembly, which are fundamentally different processes. This is a hallucination.
Claim: "Binding to the mitochondrial acyl carrier protein suggests a role in stabilizing the ACP module"
PARTIALLY CORRECT but overspecified: NDUFAB1 (the acyl carrier protein) is a different Complex I subunit. NDUFB1 does not directly bind ACP. The BioReason model confused NDUFB1 with NDUFAB1 (note the similar names).
Claim: "Contacts with NDUFB11, NDUFB5, NDUFB10, and NDUFB4 indicate lateral packing"
CORRECT: These are verified neighboring subunits in the beta subcomplex based on structural data.
Claim: "associations with NDUFA1, NDUFA2, NDUFA6, NDUFA8, and C2"
PARTIALLY CORRECT but overspecified: Some of these contacts are correct from structural data, but the specific claim of direct contacts with all of these subunits is not well-supported for the tiny NDUFB1 subunit specifically.
Claim about "quinone-access channel" stabilization
The ISO annotation for nuclear speck is transferred from human O75438. This is a questionable annotation for a mitochondrial inner membrane protein. It may derive from a high-throughput localization study with false positives, or from the small protein being detected in nuclear fractions. This should be treated skeptically.
Source: Ndufb1-deep-research-bioreason-sft.md
The BioReason functional summary describes Ndufb1 as:
A small, single-pass inner-membrane accessory subunit of mitochondrial complex I that anchors on the matrix side to stabilize the membrane arm and organize neighboring subunits around the quinone-reactive region. By scaffolding assembly intermediates and maintaining the geometry of the electron-transfer module, it supports the transfer of electrons from NADH to ubiquinone and couples this chemistry to proton pumping, thereby sustaining oxidative phosphorylation. Its assembly-stabilizing role likely extends to the integrity of adjacent respiratory supercomplexes.
This summary is broadly correct in its general characterization of NDUFB1 as a small accessory subunit of Complex I, but contains several errors of specificity and one significant factual mistake.
Correctness issues:
"Organize neighboring subunits around the quinone-reactive region" is incorrect. NDUFB1 is located in the membrane arm near core subunit ND4, which is in the proton-pumping region of Complex I, not near the quinone-reactive region. The quinone-binding site is located at the interface of the peripheral and membrane arms, near ND1 and NDUFS2/NDUFS7. NDUFB1 is several subunits away from this site. The BioReason model appears to have conflated the general membrane arm with the quinone-access channel.
"Its assembly-stabilizing role likely extends to the integrity of adjacent respiratory supercomplexes" is speculative. While Complex I does form supercomplexes (respirasomes) with Complex III and IV, there is no evidence that NDUFB1 specifically plays a role in supercomplex stability beyond being a structural subunit of Complex I itself. The BioReason thinking trace goes further, claiming involvement in "GO:0034551 mitochondrial respiratory chain complex III assembly," which is outright wrong -- NDUFB1 is a Complex I subunit with no demonstrated role in Complex III assembly.
"Binding to the mitochondrial acyl carrier protein" is incorrect. The thinking trace states that NDUFB1 binds to the mitochondrial acyl carrier protein, suggesting a role in stabilizing the ACP module. This appears to be a confusion between NDUFB1 and NDUFAB1 (also known as SDAP/ACP). These are different proteins with similar names: NDUFB1 is a 57-amino-acid transmembrane subunit, while NDUFAB1 is an acyl carrier protein that is itself a Complex I subunit. No evidence supports direct NDUFB1-ACP binding.
Overstated interaction network. The thinking trace claims "associations with NDUFA1, NDUFA2, NDUFA6, NDUFA8, and C2." While NDUFB1 does contact some neighboring subunits in the membrane arm (confirmed: NDUFB4, NDUFB5, NDUFB8, NDUFB11), the claimed contacts with the listed NDUFA subunits are not well-supported for NDUFB1 specifically. Some of these subunits are in different regions of Complex I.
What was correct:
The UniProt summary states:
Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. Essential for the catalytic activity of complex I. Essential for oxidative phosphorylation.
The UniProt summary is more conservative and accurate. Notably, it states NDUFB1 is "believed not to be involved in catalysis," which the BioReason model respects. However, the UniProt claim that NDUFB1 is "Essential for the catalytic activity of complex I" and "Essential for oxidative phosphorylation" appears to derive from the human ortholog data (PMID:27626371, Stroud et al. 2016), where systematic knockout of accessory subunits showed they are generally essential. Whether this has been specifically demonstrated for NDUFB1 alone (versus being inferred from family-wide knockout studies) requires careful reading of the Stroud et al. data.
The thinking trace reveals several characteristic issues:
Incorrect GO term suggestion. The trace explicitly mentions "GO:0034551 mitochondrial respiratory chain complex III assembly" as a function of NDUFB1. This is a Complex III assembly term applied to a Complex I subunit, which is clearly wrong. The model appears to have reasoned from "supercomplex interactions between Complex I and Complex III" to "Complex III assembly," an invalid logical leap.
Name confusion between NDUFB1 and NDUFAB1. The claim about "binding to the mitochondrial acyl carrier protein" strongly suggests the model confused the similar-sounding subunit names NDUFB1 (the subject protein) and NDUFAB1 (the acyl carrier protein). This is a classic string-similarity error.
Appropriate domain reasoning. The initial reasoning from the IPR012575 domain covering the full protein to a structural/accessory role is sound and correctly identifies the non-catalytic nature of the subunit.
Empty GO term prediction sections. Despite the narrative discussion, the structured GO term prediction sections (Molecular Function, Biological Process, Cellular Component) are all blank, indicating the model did not output structured predictions, only narrative text.
The BioReason prediction is moderately accurate for this well-characterized protein. The core identity as a Complex I accessory subunit in the mitochondrial inner membrane is correct, and the general structural role is appropriately described. However, the model makes two significant errors: (1) incorrectly placing NDUFB1 near the quinone-reactive region and claiming a role in Complex III assembly, and (2) confusing NDUFB1 with NDUFAB1 regarding acyl carrier protein binding. For a protein whose function is relatively well-established through cryo-EM structures and systematic knockout studies, these errors are avoidable and reflect the model's tendency to over-elaborate beyond what the evidence supports.
id: P0DN34
gene_symbol: Ndufb1
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:10090
label: Mus musculus
description: >-
Ndufb1 (MNLL) is one of the smallest accessory subunits of mitochondrial
NADH:ubiquinone oxidoreductase (Complex I), a 45-subunit enzyme of the
inner mitochondrial membrane that transfers electrons from NADH to
ubiquinone and couples this to proton translocation. The 57-amino-acid
protein contains a single transmembrane helix that anchors it in the
membrane arm near the core subunit ND4, with a short C-terminal domain
exposed to the mitochondrial matrix. As a non-catalytic accessory subunit,
Ndufb1 contributes to the structural integrity of Complex I and is
incorporated during the ND4-module stage of the modular assembly pathway.
Cryo-EM structures from mouse heart mitochondria confirm its position in
the membrane domain, where it contacts neighboring beta-subcomplex subunits
NDUFB4, NDUFB5, NDUFB8, and NDUFB11.
existing_annotations:
- term:
id: GO:0045271
label: respiratory chain complex I
qualifier: part_of
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
Phylogenetic inference that Ndufb1 is part of respiratory chain complex I.
Consistent with all structural and biochemical evidence showing NDUFB1 as
an integral subunit of Complex I across eukaryotes.
action: ACCEPT
supported_by:
- reference_id: PMID:38575788
supporting_text: >-
Supercomplexes of the respiratory chain...mammalian (mouse) tissues
contain three defined types of 'respirasome', supercomplexes made of
CI, CIII2 and CIV
- term:
id: GO:0005739
label: mitochondrion
qualifier: located_in
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
Automated annotation placing Ndufb1 in the mitochondrion. Correct but
less specific than the mitochondrial inner membrane annotation which is
also present. Subsumed by the more specific localization.
action: KEEP_AS_NON_CORE
supported_by:
- reference_id: PMID:38575788
supporting_text: >-
Supercomplexes of the respiratory chain...mammalian (mouse) tissues
contain three defined types of 'respirasome'
- term:
id: GO:0005743
label: mitochondrial inner membrane
qualifier: located_in
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
Automated annotation for mitochondrial inner membrane localization.
Correct and supported by direct structural evidence from cryo-EM of
mouse Complex I showing NDUFB1 embedded in the inner membrane with a
single transmembrane helix.
action: ACCEPT
supported_by:
- reference_id: PMID:38575788
supporting_text: >-
Supercomplexes of the respiratory chain...mammalian (mouse) tissues
contain three defined types of 'respirasome', supercomplexes made of
CI, CIII2 and CIV
- term:
id: GO:0045271
label: respiratory chain complex I
qualifier: part_of
evidence_type: IEA
original_reference_id: GO_REF:0000107
review:
summary: >-
Ensembl Compara-based transfer from human ortholog. Correct and
redundant with the IBA and IDA annotations for the same term.
action: ACCEPT
supported_by:
- reference_id: PMID:38575788
supporting_text: >-
Supercomplexes of the respiratory chain...mammalian (mouse) tissues
contain three defined types of 'respirasome', supercomplexes made of
CI, CIII2 and CIV
- term:
id: GO:0005739
label: mitochondrion
qualifier: located_in
evidence_type: ISO
original_reference_id: GO_REF:0000119
review:
summary: >-
Manual transfer from human ortholog O75438. Correct but less specific
than the inner membrane annotation.
action: KEEP_AS_NON_CORE
supported_by:
- reference_id: PMID:38575788
supporting_text: >-
Supercomplexes of the respiratory chain...mammalian (mouse) tissues
contain three defined types of 'respirasome'
- term:
id: GO:0005743
label: mitochondrial inner membrane
qualifier: located_in
evidence_type: ISO
original_reference_id: GO_REF:0000119
review:
summary: >-
Manual transfer from human ortholog O75438 for mitochondrial inner
membrane localization. Correct, and confirmed directly in mouse by
cryo-EM (PMID:38575788).
action: ACCEPT
supported_by:
- reference_id: PMID:38575788
supporting_text: >-
Supercomplexes of the respiratory chain...mammalian (mouse) tissues
contain three defined types of 'respirasome', supercomplexes made of
CI, CIII2 and CIV
- term:
id: GO:0045271
label: respiratory chain complex I
qualifier: part_of
evidence_type: ISO
original_reference_id: GO_REF:0000119
review:
summary: >-
Manual transfer from human ortholog. Correct and redundant with IDA
and IBA annotations for the same term.
action: ACCEPT
supported_by:
- reference_id: PMID:38575788
supporting_text: >-
Supercomplexes of the respiratory chain...mammalian (mouse) tissues
contain three defined types of 'respirasome', supercomplexes made of
CI, CIII2 and CIV
- term:
id: GO:0016607
label: nuclear speck
qualifier: located_in
evidence_type: ISO
original_reference_id: GO_REF:0000119
review:
summary: >-
Transfer from human ortholog O75438 for nuclear speck localization.
This is a questionable annotation for a well-characterized mitochondrial
inner membrane protein. NDUFB1 is a single-pass transmembrane protein
that is an integral part of the membrane arm of Complex I. No published
study has demonstrated dual mitochondrial/nuclear localization for this
protein. The human annotation may derive from a high-throughput study
with false-positive nuclear detections, possibly due to the very small
size of the protein (57 aa) leading to mislocalization artifacts.
action: MARK_AS_OVER_ANNOTATED
reason: >-
No credible evidence supports nuclear speck localization for a small
transmembrane Complex I subunit. Likely a false positive from
high-throughput localization screening.
- term:
id: GO:0009060
label: aerobic respiration
qualifier: involved_in
evidence_type: NAS
original_reference_id: PMID:30030361
review:
summary: >-
ComplexPortal annotation based on the review by Signes and
Fernandez-Vizarra 2018. As a structural subunit of Complex I, NDUFB1
participates in the respiratory chain and therefore in aerobic
respiration. The term is correct but broad; the more specific process
is mitochondrial electron transport from NADH to ubiquinone.
action: KEEP_AS_NON_CORE
supported_by:
- reference_id: PMID:30030361
supporting_text: >-
The assembly of the five oxidative phosphorylation system (OXPHOS)
complexes in the inner mitochondrial membrane is an intricate
process
- term:
id: GO:0042776
label: proton motive force-driven mitochondrial ATP synthesis
qualifier: involved_in
evidence_type: NAS
original_reference_id: PMID:30030361
review:
summary: >-
ComplexPortal annotation. Complex I contributes to the proton motive
force by pumping protons across the inner membrane, which drives ATP
synthase. NDUFB1 as a structural subunit contributes indirectly to
this process. However, NDUFB1 itself is not in the proton-pumping
modules directly; it is a structural element. The annotation is not
wrong but represents an indirect contribution.
action: KEEP_AS_NON_CORE
supported_by:
- reference_id: PMID:30030361
supporting_text: >-
The assembly of the five oxidative phosphorylation system (OXPHOS)
complexes in the inner mitochondrial membrane is an intricate
process
- term:
id: GO:0005743
label: mitochondrial inner membrane
qualifier: is_active_in
evidence_type: IDA
original_reference_id: PMID:38575788
review:
summary: >-
Direct experimental evidence from cryo-EM of mouse heart mitochondria
showing NDUFB1 as part of Complex I in the inner membrane. The
is_active_in qualifier is appropriate since this is where the protein
functions as part of the respirasome.
action: ACCEPT
supported_by:
- reference_id: PMID:38575788
supporting_text: >-
mammalian (mouse) tissues contain three defined types of
'respirasome', supercomplexes made of CI, CIII2 and CIV
- term:
id: GO:0045271
label: respiratory chain complex I
qualifier: part_of
evidence_type: IDA
original_reference_id: PMID:38575788
review:
summary: >-
Direct experimental evidence from cryo-EM structures of mouse
respirasomes. Ndufb1 is resolved as chain f in the Complex I structure.
This is the strongest evidence for this annotation.
action: ACCEPT
supported_by:
- reference_id: PMID:38575788
supporting_text: >-
mammalian (mouse) tissues contain three defined types of
'respirasome', supercomplexes made of CI, CIII2 and CIV
- term:
id: GO:0045271
label: respiratory chain complex I
qualifier: part_of
evidence_type: ISS
original_reference_id: GO_REF:0000024
review:
summary: >-
Manual sequence similarity-based transfer. Correct and consistent with
direct experimental evidence from mouse cryo-EM studies.
action: ACCEPT
supported_by:
- reference_id: PMID:38575788
supporting_text: >-
mammalian (mouse) tissues contain three defined types of
'respirasome', supercomplexes made of CI, CIII2 and CIV
- term:
id: GO:0005198
label: structural molecule activity
qualifier: enables
evidence_type: ISS
review:
summary: >-
NDUFB1 is a non-catalytic accessory subunit of Complex I. It lacks any
catalytic motifs and its role is structural: stabilizing the membrane
arm of Complex I around the ND4 core subunit. Structural molecule
activity is the appropriate molecular function for accessory subunits
that contribute to complex integrity without independent enzymatic
activity.
action: NEW
reason: >-
No molecular function annotation currently exists for Ndufb1. As a
non-catalytic accessory subunit, structural molecule activity is the
most appropriate MF term.
supported_by:
- reference_id: PMID:38575788
supporting_text: >-
mammalian (mouse) tissues contain three defined types of
'respirasome', supercomplexes made of CI, CIII2 and CIV
- reference_id: PMID:27626371
supporting_text: >-
Complex I (NADH:ubiquinone oxidoreductase) is the first enzyme of the
mitochondrial respiratory chain and is composed of 45 subunits in
humans
- reference_id: file:mouse/Ndufb1/Ndufb1-deep-research-bioreason-sft.md
supporting_text: >-
A small, non-catalytic accessory subunit tailored to the membrane arm
of respiratory complex I...This architecture causes the protein to
function as a structural and organizational element rather than as an
active redox catalyst
- term:
id: GO:0032981
label: mitochondrial respiratory chain complex I assembly
qualifier: involved_in
evidence_type: ISS
review:
summary: >-
NDUFB1 is incorporated during the ND4-module stage of Complex I
assembly. Systematic studies of accessory subunits in human cells
(PMID:27626371) demonstrate that loss of accessory subunits disrupts
Complex I assembly. NDUFB1 is part of the ND4-module assembly
intermediate along with NDUFB4, NDUFB5, NDUFB6, NDUFB10, NDUFB11.
action: NEW
reason: >-
No Complex I assembly annotation is present despite evidence that
NDUFB1 is part of a defined assembly intermediate (ND4-module).
supported_by:
- reference_id: PMID:27626371
supporting_text: >-
Complex I (NADH:ubiquinone oxidoreductase) is the first enzyme of the
mitochondrial respiratory chain and is composed of 45 subunits in
humans
- reference_id: PMID:30030361
supporting_text: >-
The human enzymes comprise core proteins, performing the catalytic
activities, and a large number of 'supernumerary' subunits that play
essential roles in assembly, regulation and stability
- term:
id: GO:0006120
label: mitochondrial electron transport, NADH to ubiquinone
qualifier: involved_in
evidence_type: NAS
original_reference_id: PMID:30030361
review:
summary: >-
As a structural subunit of Complex I, NDUFB1 is essential for the
complex-level activity of NADH to ubiquinone electron transfer.
Although NDUFB1 itself is non-catalytic, loss of accessory subunits
abolishes Complex I activity. This is more specific than the existing
aerobic respiration annotation.
action: NEW
reason: >-
This process term more precisely describes the role of Complex I in
mitochondrial electron transport than the broader aerobic respiration
term already present.
supported_by:
- reference_id: PMID:30030361
supporting_text: >-
The assembly of the five oxidative phosphorylation system (OXPHOS)
complexes in the inner mitochondrial membrane is an intricate
process
- reference_id: PMID:38575788
supporting_text: >-
mammalian (mouse) tissues contain three defined types of
'respirasome', supercomplexes made of CI, CIII2 and CIV
references:
- id: GO_REF:0000024
title: >-
Manual transfer of experimentally-verified manual GO annotation data to
orthologs by curator judgment of sequence similarity
findings: []
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000107
title: >-
Automatic transfer of experimentally verified manual GO annotation data
to orthologs using Ensembl Compara
findings: []
- id: GO_REF:0000119
title: >-
Automated transfer of experimentally-verified manual GO annotation data
to mouse-human orthologs
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: PMID:19468303
title: >-
Lineage-specific biology revealed by a finished genome assembly of the
mouse.
findings:
- statement: Provides the genomic sequence for Ndufb1 from mouse strain C57BL/6J
supporting_text: >-
we are now able to define 20,210 protein-coding genes
reference_section_type: RESULTS
- id: PMID:30030361
title: >-
Assembly of mammalian oxidative phosphorylation complexes I-V and
supercomplexes.
findings:
- statement: >-
Review covering assembly pathways of OXPHOS complexes including Complex I
supporting_text: >-
The assembly of the five oxidative phosphorylation system (OXPHOS)
complexes in the inner mitochondrial membrane is an intricate process
reference_section_type: ABSTRACT
- statement: >-
Complex I assembly involves modular intermediates with accessory subunits
playing essential roles in assembly, regulation and stability
supporting_text: >-
The human enzymes comprise core proteins, performing the catalytic
activities, and a large number of 'supernumerary' subunits that play
essential roles in assembly, regulation and stability
reference_section_type: ABSTRACT
- id: PMID:38575788
title: >-
SCAF1 drives the compositional diversity of mammalian respirasomes.
findings:
- statement: >-
Cryo-EM structures of three types of mouse respirasomes resolved at
3.3-3.6 A, with Ndufb1 visible as chain f in Complex I
supporting_text: >-
mammalian (mouse) tissues contain three defined types of
'respirasome', supercomplexes made of CI, CIII2 and CIV
reference_section_type: ABSTRACT
- statement: >-
SCAF1 is associated with one type of respirasome, demonstrating
compositional diversity of supercomplexes
supporting_text: >-
The stoichiometry and position of CIV differs in the three
respirasomes, of which only one contains the supercomplex-associated
factor SCAF1
reference_section_type: ABSTRACT
- id: PMID:27626371
title: >-
Accessory subunits are integral for assembly and function of human
mitochondrial complex I.
findings:
- statement: >-
Systematic CRISPR knockout of all 31 accessory subunits shows they are
essential for Complex I assembly and function
supporting_text: >-
Complex I (NADH:ubiquinone oxidoreductase) is the first enzyme of the
mitochondrial respiratory chain and is composed of 45 subunits in
humans
reference_section_type: ABSTRACT
- id: file:mouse/Ndufb1/Ndufb1-notes.md
title: Research notes on Ndufb1
findings:
- statement: >-
NDUFB1 is part of the ND4-module assembly intermediate in the modular
Complex I assembly pathway
- statement: >-
BioReason deep research contains errors including confusion of Complex I
with Complex III assembly and NDUFB1 with NDUFAB1
core_functions:
- description: >-
Ndufb1 serves as a structural accessory subunit of mitochondrial Complex I,
stabilizing the membrane arm in the region around core subunit ND4. It is
incorporated during the ND4-module stage of the modular Complex I assembly
pathway. The single transmembrane helix anchors the protein in the inner
membrane, with its C-terminal domain contacting neighboring subunits
NDUFB4, NDUFB5, NDUFB8, and NDUFB11 on the matrix side. As an accessory
subunit, it contributes to the complex-level NADH dehydrogenase activity
but does not itself catalyze any reaction.
molecular_function:
id: GO:0005198
label: structural molecule activity
contributes_to_molecular_function:
id: GO:0008137
label: NADH dehydrogenase (ubiquinone) activity
directly_involved_in:
- id: GO:0032981
label: mitochondrial respiratory chain complex I assembly
- id: GO:0006120
label: mitochondrial electron transport, NADH to ubiquinone
locations:
- id: GO:0005743
label: mitochondrial inner membrane
in_complex:
id: GO:0045271
label: respiratory chain complex I
supported_by:
- reference_id: PMID:38575788
supporting_text: >-
mammalian (mouse) tissues contain three defined types of
'respirasome', supercomplexes made of CI, CIII2 and CIV
- reference_id: PMID:30030361
supporting_text: >-
The human enzymes comprise core proteins, performing the catalytic
activities, and a large number of 'supernumerary' subunits that play
essential roles in assembly, regulation and stability
- reference_id: PMID:27626371
supporting_text: >-
Complex I (NADH:ubiquinone oxidoreductase) is the first enzyme of the
mitochondrial respiratory chain and is composed of 45 subunits in
humans
suggested_questions:
- question: >-
What is the specific phenotype of Ndufb1 knockout in mouse cells or
tissues? Does loss of NDUFB1 lead to complete loss of Complex I, or is
a partially assembled complex retained?
experts:
- Stroud DA
- question: >-
Does NDUFB1 have any role in stabilizing respiratory supercomplexes
(respirasomes) beyond its role within Complex I itself?
experts:
- Sazanov LA
- Vercellino I
suggested_experiments:
- description: >-
CRISPR knockout of Ndufb1 in mouse cell lines followed by complexome
profiling to determine whether loss of NDUFB1 specifically disrupts
the ND4-module assembly intermediate or affects broader Complex I
stability.
experiment_type: complexome profiling
- description: >-
Crosslinking mass spectrometry of purified mouse Complex I to map the
direct protein-protein contacts of NDUFB1 and determine whether it
bridges the ND4-module to adjacent assembly modules.
experiment_type: XL-MS