TIM9 is a small mitochondrial intermembrane space (IMS) chaperone that forms a hexameric complex with TIM10 (the Tim9-Tim10 or TIM10 complex, composed of 3 copies of each subunit). This soluble 70 kDa complex functions as a carrier-holdase that escorts hydrophobic transmembrane protein precursors, especially mitochondrial carriers, from the TOM complex across the aqueous IMS to the TIM22 complex for insertion into the inner membrane. Small Tim complexes have also been implicated in delivery of some beta-barrel precursors toward the SAM complex. TIM9 contains a twin CX3C motif that forms two intramolecular disulfide bonds in the IMS; during cytoplasmic transit these cysteines may coordinate zinc. TIM9 is essential for viability and plays both a structural role in complex assembly and a functional role in substrate recognition, with its N-terminal region required for efficient trapping of incoming substrates.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005743 mitochondrial inner membrane | IBA GO_REF:0000033 | ACCEPT | Summary: TIM9 is a peripheral membrane protein on the IMS face of the mitochondrial inner membrane (PMID:9822593, PMID:9889188). The IBA annotation to mitochondrial inner membrane is phylogenetically consistent and supported by experimental evidence in yeast. UniProt records the subcellular location as "Mitochondrion inner membrane; Peripheral membrane protein; Intermembrane side." Reason: TIM9 is well-established as associated with the mitochondrial inner membrane, where a fraction of Tim9 is part of the membrane-associated 300 kDa TIM22 complex (PMID:9822593). The IBA annotation is phylogenetically sound and consistent with the IDA annotations. Propagation Review Root cause: SOURCE STALE OR MISSING Sources checked: PANTHER:PTN004407763 · PANTHER:PTN004407763 SOURCE STALE OR MISSING This retired GOA row traced mitochondrial-inner-membrane location to PTN004407763; current PAINT no longer carries GO:0005743 at this node. Supporting Evidence: PMID:9822593 A small fraction of Tim9p is bound to the outer face of the inner membrane in a 300 kDa complex whose other subunits include Tim54p, Tim22p, Tim12p and Tim10p. PMID:9889188 Tim9 is located in the mitochondrial intermembrane space and is organized into two distinct hetero-oligomeric assemblies with Tim10 and Tim12. |
| GO:0045039 protein insertion into mitochondrial inner membrane | IBA GO_REF:0000033 | ACCEPT | Summary: The Tim9-Tim10 complex escorts carrier protein precursors across the IMS to the TIM22 complex for insertion into the inner membrane. This is a core function of TIM9, supported by multiple experimental studies (PMID:9822593, PMID:9889188, PMID:10469659, PMID:11483513). The IBA annotation is phylogenetically consistent. Reason: This is the core biological process that TIM9 participates in. The Tim9-Tim10 complex mediates partial translocation of mitochondrial carrier proteins across the outer membrane and their subsequent insertion into the inner membrane via TIM22 (PMID:9889188). Multiple experimental evidence codes support this for yeast TIM9 directly. Propagation Review Root cause: SOURCE STALE OR MISSING Sources checked: PANTHER:PTN004407763 · PANTHER:PTN004407763 SOURCE STALE OR MISSING This retired GOA row traced inner-membrane-insertion process to PTN004407763; current PAINT no longer carries GO:0045039 at this node. Supporting Evidence: PMID:9889188 The TIM9.10 complex is more abundant than the TIM9.10.12 complex and mediates partial translocation of mitochondrial carriers proteins across the outer membrane. PMID:9822593 Tim9p is a new subunit of the TIM machinery that guides hydrophobic inner membrane proteins across the aqueous intermembrane space. file:yeast/TIM9/TIM9-deep-research-falcon.md Tim9 acts as a **chaperone/escort factor** that prevents aggregation of hydrophobic precursors in the aqueous IMS and transfers them from **TOM** to **TIM22**. |
| GO:0140318 protein transporter activity | IBA GO_REF:0000033 | MODIFY | Summary: This retired IBA captured the real Tim9-Tim10 shuttle, but current PAINT has narrowed the PTN004407763 assertion from broad protein transporter activity to unfolded protein holdase activity. Reason: GO:0140309 now captures both the holdase and escort dimensions of the Tim9-Tim10 shuttle: it binds unfolded hydrophobic precursors, prevents their aggregation in the aqueous IMS, and escorts them toward acceptor translocases. Replace the stale broad GO:0140318 transfer with this specific current PAINT term. Propagation Review Root cause: SOURCE STALE OR MISSING Sources checked: PANTHER:PTN004407763 · PANTHER:PTN004407763 SOURCE STALE OR MISSING This retired GOA row traced broad protein-transporter activity to PTN004407763; current PAINT now places GO:0140309 holdase activity, not GO:0140318, at this node. Proposed replacements: unfolded protein holdase activity Supporting Evidence: PMID:9822593 Tim9p is a new subunit of the TIM machinery that guides hydrophobic inner membrane proteins across the aqueous intermembrane space. |
| GO:0005743 mitochondrial inner membrane | IEA GO_REF:0000044 | ACCEPT | Summary: IEA annotation mapping from UniProtKB subcellular location. TIM9 is annotated in UniProt as "Mitochondrion inner membrane; Peripheral membrane protein; Intermembrane side." This is consistent with experimental evidence. Reason: This IEA is broader than the IBA and IDA annotations for the same term and is consistent with the known localization of TIM9 at the mitochondrial inner membrane (PMID:9822593). Supporting Evidence: UniProt:O74700 SUBCELLULAR LOCATION: Mitochondrion inner membrane |
| GO:0005758 mitochondrial intermembrane space | IEA GO_REF:0000044 | ACCEPT | Summary: IEA annotation mapping from UniProtKB subcellular location. TIM9 is localized to the mitochondrial intermembrane space where it forms the soluble Tim9-Tim10 70 kDa complex. Well supported by experimental evidence. Reason: The IMS localization is well-established experimentally (PMID:9822593, PMID:9889188) and confirmed by proteomics (PMID:22984289, cited in UniProt). The IEA is consistent with direct evidence. Supporting Evidence: PMID:9889188 Tim9 is located in the mitochondrial intermembrane space and is organized into two distinct hetero-oligomeric assemblies with Tim10 and Tim12. file:yeast/TIM9/TIM9-deep-research-falcon.md Tim9 is located in the **mitochondrial IMS** |
| GO:0015031 protein transport | IEA GO_REF:0000043 | KEEP AS NON CORE | Summary: IEA annotation from UniProtKB keyword mapping (KW-0653 Protein transport, KW-0811 Translocation). TIM9 participates in protein transport across the IMS. This is a general parent term; the more specific GO:0045039 (protein insertion into mitochondrial inner membrane) is also annotated. Reason: This umbrella is correct, but it is less informative than the reviewed transporter, holdase, and inner-membrane-insertion terms. It also accommodates the less directly documented SAM-directed route, so it is retained as non-core rather than narrowed to only one destination. Supporting Evidence: UniProt:O74700 Mitochondrial intermembrane chaperone that participates in the import and insertion of multi-pass transmembrane proteins into the mitochondrial inner membrane. |
| GO:0042719 mitochondrial intermembrane space chaperone complex | IEA GO_REF:0000117 | ACCEPT | Summary: IEA annotation from ARBA machine learning. TIM9 is a component of the mitochondrial intermembrane space chaperone complex (the Tim9-Tim10 hexameric complex). Well supported by experimental evidence. Reason: This IEA is consistent with the IDA annotations for the same term (PMID:9822593, PMID:9889188). TIM9 is a canonical subunit of the IMS chaperone complex. Falcon deep research independently confirms the Tim9-Tim10 heterohexamer with 3:3 stoichiometry (~70 kDa soluble complex). Supporting Evidence: PMID:9822593 Most of Tim9p is associated with Tim10p in a soluble 70 kDa complex. file:yeast/TIM9/TIM9-deep-research-falcon.md Tim9 forms the canonical **Tim9–Tim10 heterohexamer** and also participates in a **Tim9–Tim10–Tim12 docking complex** linked to TIM22. file:yeast/TIM9/TIM9-deep-research-falcon.md Tim9:Tim10 complex stoichiometry is **3:3**; the TIM22-associated complex is **Tim9–Tim10–Tim12 = 3:2:1**; the soluble Tim9/Tim10 complex is about **~70 kDa** |
| GO:0046872 metal ion binding | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | Summary: IEA annotation from UniProtKB keyword mapping (KW-0479 Metal-binding). TIM9 has a twin CX3C motif with four conserved cysteines. However, in the mature IMS-localized form, these cysteines form disulfide bonds rather than coordinating metal ions. Zinc coordination is thought to occur only transiently during cytoplasmic transit, and the mature functional form does not bind zinc (PMID:11867522). This IEA is misleading for the functional state of TIM9. Reason: While TIM9 may transiently coordinate zinc during its own import through the TOM complex, the mature functional form in the IMS contains disulfide bonds rather than zinc-coordinated cysteines (PMID:11867522). The UniProt entry itself states that the twin CX3C motif "contains 4 conserved Cys residues that form 2 disulfide bonds in the mitochondrial intermembrane space" and zinc coordination is only probable during transit. Annotating TIM9 as a metal ion binding protein is misleading for its functional state. Supporting Evidence: UniProt:O74700 The twin CX3C motif contains 4 conserved Cys residues that form 2 disulfide bonds in the mitochondrial intermembrane space. However, during the transit of TIM9 from cytoplasm into mitochondrion, the Cys residues probably coordinate zinc, thereby preventing folding and allowing its transfer across mitochondrial outer membrane file:yeast/TIM9/TIM9-deep-research-falcon.md Small TIM proteins (including Tim9) are imported through TOM and undergo oxidative folding in the IMS via the **MIA (mitochondrial import and assembly) pathway**, which introduces disulfides in the conserved CX3C motifs |
| GO:0005515 protein binding | IPI PMID:11483513 Functional reconstitution of the import of the yeast ADP/ATP... | REMOVE | Summary: IPI annotation based on physical interaction with TIM10 (PMID:11483513). Tim9 and Tim10 purified from E. coli can form a complex of the same size as the endogenous complex. This demonstrates direct protein-protein interaction. However, "protein binding" is uninformative -- TIM9 binding to TIM10 reflects its role in forming the functional hexameric chaperone complex. Reason: GO:0005515 "protein binding" is too vague to carry forward as a functional annotation. The Tim9-Tim10 interaction itself is real, but the specific biology is TIM9's membership in the mitochondrial IMS chaperone complex and its contribution to holdase/transporter activity in the assembled heterohexamer. This IPI evidence does not require a separate generic protein-binding assertion. Supporting Evidence: PMID:11483513 Tim9 and Tim10 purified from Escherichia coli can form a complex of the same size as the endogenous complex from yeast mitochondria. This shows that no other mitochondrial protein is required for the formation of the TIM10 complex. file:yeast/TIM9/TIM9-deep-research-falcon.md Tim9 and Tim10 assemble into an essential heterohexameric Tim9/10 complex** that chaperones hydrophobic preproteins from TOM to TIM22 file:yeast/TIM9/TIM9-deep-research-falcon.md Biochemical substrate-binding evidence indicates that **Tim10** (alone) can bind the **ATP/ADP carrier (AAC)** similarly to the Tim9–Tim10 complex, whereas **Tim9 alone does not bind AAC**, supporting a model where Tim10 provides key substrate-binding elements within the complex |
| GO:0005739 mitochondrion | IDA PMID:9889188 Tim9, a new component of the TIM22.54 translocase in mitocho... | ACCEPT | Summary: IDA annotation for mitochondrial localization of TIM9 based on Adam et al. (1999), who identified Tim9 as a new component of the TIM22.54 translocase and demonstrated its mitochondrial localization. Reason: TIM9 is a well-established mitochondrial protein. This IDA is correct and supported by direct experimental evidence. Supporting Evidence: PMID:9889188 Tim9 is located in the mitochondrial intermembrane space and is organized into two distinct hetero-oligomeric assemblies with Tim10 and Tim12. |
| GO:0005743 mitochondrial inner membrane | IDA PMID:10648604 Tim18p, a new subunit of the TIM22 complex that mediates ins... | ACCEPT | Summary: IDA annotation for mitochondrial inner membrane localization based on Koehler et al. (2000), who characterized the TIM22 complex in the inner membrane containing Tim9p among its peripheral subunits. Reason: A fraction of TIM9 is associated with the inner membrane as part of the 300 kDa TIM22 complex. This is consistent with the UniProt annotation and the known biology of TIM9. Supporting Evidence: PMID:10648604 The TIM22 complex contains the peripheral subunits Tim9p, Tim10p, and Tim12p and the integral membrane subunits Tim22p and Tim54p. |
| GO:0005758 mitochondrial intermembrane space | IDA PMID:19037698 The Dutch multicenter experience of the endo-sponge treatmen... | ACCEPT | Summary: IDA annotation for IMS localization. However, PMID:19037698 is about "The Dutch multicenter experience of the endo-sponge treatment for anastomotic leakage after colorectal surgery" -- this is clearly an incorrect PMID. The intended reference is likely PMID:19037098 (Baker et al. 2009, about Tim9-Tim10 complex structure and function). The annotation itself is correct -- TIM9 is localized to the IMS -- but the reference is wrong. Reason: The localization of TIM9 to the mitochondrial IMS is well-established by multiple independent studies (PMID:9822593, PMID:9889188). Although the cited PMID:19037698 appears to be a data entry error (likely meant PMID:19037098), the annotation itself is correct. Note: the PMID should be corrected from 19037698 to 19037098. Supporting Evidence: PMID:9822593 Most of Tim9p is associated with Tim10p in a soluble 70 kDa complex. PMID:19037098 The Tim9-Tim10 complex plays an essential role in mitochondrial protein import by chaperoning select hydrophobic precursor proteins across the intermembrane space. |
| GO:0045039 protein insertion into mitochondrial inner membrane | IDA PMID:10648604 Tim18p, a new subunit of the TIM22 complex that mediates ins... | ACCEPT | Summary: IDA annotation based on Koehler et al. (2000), who showed that Tim9p is part of the TIM22 complex mediating insertion of carrier proteins into the inner membrane. Deletion of TIM18 (a TIM22 complex subunit) is synthetically lethal with temperature-sensitive mutations in Tim9p. Reason: This is a core function of TIM9. The Tim9-Tim10 complex escorts carrier proteins to the TIM22 complex for insertion into the inner membrane. Supporting Evidence: PMID:10648604 Deletion of Tim18p decreases the growth rate of yeast cells by a factor of two and is synthetically lethal with temperature-sensitive mutations in Tim9p or Tim10p. |
| GO:0045039 protein insertion into mitochondrial inner membrane | IDA PMID:19037098 Structural and functional requirements for activity of the T... | ACCEPT | Summary: IDA annotation based on Baker et al. (2009), who solved the Tim9-Tim10 crystal structure at 2.5 A resolution and performed mutational analysis showing that Tim9 plays an important functional role in facilitating the initial steps of translocating precursor substrates into the IMS. Reason: Baker et al. provide structural and functional evidence that Tim9 is directly involved in substrate recognition and translocation, not just complex stabilization. Supporting Evidence: PMID:19037098 We conclude that Tim9 plays an important functional role that includes facilitating the initial steps in translocating precursor substrates into the intermembrane space. |
| GO:0008270 zinc ion binding | RCA PMID:30358795 The cellular economy of the Saccharomyces cerevisiae zinc pr... | MARK AS OVER ANNOTATED | Summary: RCA annotation for zinc ion binding from Wang et al. (2018), a study characterizing the yeast zinc proteome by bioinformatic domain and motif searches. TIM9 was identified as a potential zinc-binding protein based on its CX3C motif. However, experimental evidence from Curran et al. (2002, PMID:11867522) demonstrated that TIM9 in the mature IMS form contains disulfide bonds, not zinc-coordinated cysteines. Reason: The RCA annotation is based on computational prediction from the CX3C motif. While TIM9 may transiently bind zinc during its cytoplasmic import phase, the mature functional form in the IMS uses disulfide bonds rather than zinc coordination (PMID:11867522, cited in UniProt). The annotation to GO:0008270 is misleading for the steady-state functional protein. Supporting Evidence: UniProt:O74700 The twin CX3C motif contains 4 conserved Cys residues that form 2 disulfide bonds in the mitochondrial intermembrane space. However, during the transit of TIM9 from cytoplasm into mitochondrion, the Cys residues probably coordinate zinc PMID:30358795 The yeast zinc proteome of 582 known or potential zinc-binding proteins was identified using a bioinformatics analysis that combined global domain searches with local motif searches. file:yeast/TIM9/TIM9-deep-research-falcon.md the conserved **CX3C** cysteines form **two intramolecular disulfide bonds** important for structural integrity |
| GO:0005758 mitochondrial intermembrane space | TAS Reactome:R-SCE-1252259 | ACCEPT | Summary: TAS annotation from Reactome pathway "TIM9:TIM10 binds hydrophobic proteins." The IMS localization is consistent with all experimental evidence. Reason: Correctly reflects the localization of TIM9 in the IMS as part of the Tim9-Tim10 complex. Redundant with IDA annotations but not incorrect. Supporting Evidence: Reactome:R-SCE-1252259 TIM9:TIM10 binds hydrophobic proteins |
| GO:0005758 mitochondrial intermembrane space | TAS Reactome:R-SCE-1252260 | ACCEPT | Summary: TAS annotation from Reactome pathway "MIA40:ERV1 oxidizes cysteine residues to cystine disulfide bonds." This Reactome entry relates to the MIA pathway by which TIM9 is imported and oxidized in the IMS. The IMS localization is correct. Reason: The MIA pathway (Mia40/Erv1) is responsible for the oxidative folding of TIM9 in the IMS, forming the disulfide bonds in its twin CX3C motif. This correctly places TIM9 in the IMS. Redundant with other IMS localization annotations but not incorrect. Supporting Evidence: Reactome:R-SCE-1252260 MIA40:ERV1 oxidizes cysteine residues to cystine disulfide bonds |
| GO:0140318 protein transporter activity | IDA PMID:9822593 Tim9p, an essential partner subunit of Tim10p for the import... | MODIFY | Summary: IDA annotation for protein transporter activity based on Koehler et al. (1998), who demonstrated that Tim9p is an essential partner of Tim10p for the import of mitochondrial carrier proteins and can be cross-linked to partly translocated carrier proteins. Reason: Current SGD substituted the two 2019 PMID:9822593 protein-transporter rows with direct GO:0140309 rows at the same evidence dates. GO:0140309 is the more specific carrier-holdase term for the same biology, because the Tim9-Tim10 complex binds hydrophobic precursor clients and guides them through the aqueous IMS while keeping them soluble. Proposed replacements: unfolded protein holdase activity Supporting Evidence: PMID:9822593 Tim9p can be cross-linked to a partly translocated carrier protein. PMID:9822593 Tim9p is a new subunit of the TIM machinery that guides hydrophobic inner membrane proteins across the aqueous intermembrane space. |
| GO:0140318 protein transporter activity | IGI PMID:9822593 Tim9p, an essential partner subunit of Tim10p for the import... | MODIFY | Summary: IGI annotation for protein transporter activity from the same study. Tim9p function was shown through genetic interaction with Tim10p (Ser67Cys mutation in Tim9p suppresses temperature-sensitive growth defects of tim10-1 and tim12-1 mutants). Reason: The genetic interaction supports Tim9's role in the Tim9-Tim10-Tim12 carrier import pathway, and current SGD represents the same PMID:9822593 assertion as GO:0140309 rather than broad GO:0140318. The holdase term is the evidence-matched replacement because it includes escort of unfolded clients to an acceptor or location. Proposed replacements: unfolded protein holdase activity Supporting Evidence: PMID:9822593 A Ser67-->Cys67 mutation in Tim9p suppresses the temperature-sensitive growth defect of tim10-1 and tim12-1 mutants. |
| GO:0005739 mitochondrion | HDA PMID:24769239 Quantitative variations of the mitochondrial proteome and ph... | ACCEPT | Summary: HDA (high-throughput direct assay) annotation for mitochondrial localization based on Renvoise et al. (2014), a quantitative proteomic study of isolated yeast mitochondria. TIM9 was identified by mass spectrometry in mitochondrial fractions. Reason: Proteomic identification of TIM9 in mitochondrial fractions is consistent with all other evidence for its mitochondrial localization. Supporting Evidence: PMID:24769239 Label free quantitative analysis of protein accumulation revealed significant variation of 176 mitochondrial proteins |
| GO:0005739 mitochondrion | HDA PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | ACCEPT | Summary: HDA annotation for mitochondrial localization based on Reinders et al. (2006), a comprehensive mitochondrial proteomics study that identified 851 proteins in yeast mitochondria using multidimensional LC-MS/MS approaches. Reason: Mass spectrometry identification of TIM9 in purified mitochondria confirms its mitochondrial localization. The UniProt entry cites this study for subcellular location. Supporting Evidence: PMID:16823961 A total of 851 different proteins (PROMITO dataset) were identified by use of multidimensional LC-MS/MS, 1D-SDS-PAGE combined with nano-LC-MS/MS and 2D-PAGE with subsequent MALDI-mass fingerprinting. |
| GO:0042719 mitochondrial intermembrane space chaperone complex | IDA PMID:9822593 Tim9p, an essential partner subunit of Tim10p for the import... | ACCEPT | Summary: IDA annotation for membership in the mitochondrial IMS chaperone complex (the soluble Tim9-Tim10 70 kDa complex) based on Koehler et al. (1998), who co-purified Tim9p and Tim10p and showed co-immunoprecipitation. Reason: TIM9 is a canonical and essential subunit of the Tim9-Tim10 IMS chaperone complex. This is a core annotation. Supporting Evidence: PMID:9822593 Most of Tim9p is associated with Tim10p in a soluble 70 kDa complex. Tim9p and Tim10p co-purify in successive chromatographic fractionations and co-immunoprecipitated with each other. |
| GO:0042719 mitochondrial intermembrane space chaperone complex | IDA PMID:9889188 Tim9, a new component of the TIM22.54 translocase in mitocho... | ACCEPT | Summary: IDA annotation for IMS chaperone complex membership based on Adam et al. (1999), who independently identified Tim9 and showed it forms distinct complexes with Tim10 and Tim12. Reason: Independent confirmation of TIM9 as a component of the IMS chaperone complex. Supporting Evidence: PMID:9889188 Tim9 is located in the mitochondrial intermembrane space and is organized into two distinct hetero-oligomeric assemblies with Tim10 and Tim12. One complex contains Tim9 and Tim10. |
| GO:0042721 TIM22 mitochondrial import inner membrane insertion complex | IDA PMID:9495346 Carrier protein import into mitochondria mediated by the int... | ACCEPT | Summary: IDA annotation for TIM22 complex membership based on Sirrenberg et al. (1998), who showed that Tim10 and Tim12 interact with precursors and are part of a complex with Tim22 that mediates inner membrane insertion. Tim9 is annotated to this complex, but the cached paper is abstract-only and foregrounds Tim10 and Tim12 rather than Tim9, so it cannot by itself verify the TIM9 assay; subsequent direct studies place Tim9 in the TIM22-associated 300 kDa complex (PMID:9822593, PMID:9889188). Reason: TIM9 is a peripheral TIM22-pathway component via its association with Tim10 and Tim12. The annotation is independently supported by PMID:9822593, while the abstract-only original reference is not overinterpreted or treated as disproving the curator's inaccessible full-text evidence. Supporting Evidence: PMID:9495346 Tim10 and Tim12 are found in a complex with Tim22, which takes over the precursor and mediates its membrane-potential-dependent insertion into the inner membrane. PMID:9822593 A small fraction of Tim9p is bound to the outer face of the inner membrane in a 300 kDa complex whose other subunits include Tim54p, Tim22p, Tim12p and Tim10p. |
| GO:0045039 protein insertion into mitochondrial inner membrane | IDA PMID:10469659 Different import pathways through the mitochondrial intermem... | ACCEPT | Summary: IDA annotation based on Leuenberger et al. (1999), who showed that the Tim9p-Tim10p complex mediates the import of a specific subset of integral inner membrane proteins and can transfer these proteins to one of three different membrane insertion sites. Reason: This study extends the known role of TIM9 beyond carrier proteins to additional inner membrane protein substrates, demonstrating the breadth of its involvement in protein insertion into the inner membrane. Supporting Evidence: PMID:10469659 the two 70 kDa complexes each mediate the import of a different subset of integral inner membrane proteins and that they can transfer these proteins to one of three different membrane insertion sites: the TIM22 complex, the TIM23 complex or an as yet uncharacterized insertion site. |
| GO:0045039 protein insertion into mitochondrial inner membrane | IDA PMID:9822593 Tim9p, an essential partner subunit of Tim10p for the import... | ACCEPT | Summary: IDA annotation based on Koehler et al. (1998), the original identification of Tim9p as an essential partner of Tim10p for import of mitochondrial carrier proteins. Reason: Foundational study demonstrating TIM9 involvement in carrier protein import. Tim9p was shown to be cross-linkable to partly translocated carrier proteins. Supporting Evidence: PMID:9822593 Tim9p can be cross-linked to a partly translocated carrier protein. |
| GO:0045039 protein insertion into mitochondrial inner membrane | IGI PMID:9822593 Tim9p, an essential partner subunit of Tim10p for the import... | ACCEPT | Summary: IGI annotation based on genetic interaction evidence from Koehler et al. (1998). The Ser67Cys mutation in Tim9p suppresses ts growth defects of tim10-1 and tim12-1, demonstrating genetic interaction within the carrier import pathway. Reason: Genetic suppression data (Tim9p Ser67Cys suppresses tim10-1 and tim12-1) support the functional involvement of TIM9 in the carrier protein import pathway. Supporting Evidence: PMID:9822593 A Ser67-->Cys67 mutation in Tim9p suppresses the temperature-sensitive growth defect of tim10-1 and tim12-1 mutants. |
| GO:0045039 protein insertion into mitochondrial inner membrane | IMP PMID:9889188 Tim9, a new component of the TIM22.54 translocase in mitocho... | ACCEPT | Summary: IMP annotation based on Adam et al. (1999), who demonstrated that Tim9 is an essential protein and that the TIM9.10 complex mediates partial translocation of carrier proteins. Reason: Mutant phenotype evidence (essentiality and translocation defects) supports the role of TIM9 in protein insertion into the mitochondrial inner membrane. Supporting Evidence: PMID:9889188 We have identified Tim9, a new component of the TIM22.54 import machinery, which mediates transport of proteins into the inner membrane of mitochondria. Tim9, an essential protein of Saccharomyces cerevisiae |
| GO:0051082 unfolded protein binding | IDA PMID:12138093 Assembly of Tim9 and Tim10 into a functional chaperone. | MODIFY | Summary: IDA annotation for unfolded protein binding based on Vial et al. (2002), who demonstrated that the reconstituted Tim9-Tim10 complex binds to the physiological substrate ADP/ATP carrier (AAC) and displays chaperone activity in refolding the model substrate firefly luciferase. TIM9 contributes to the canonical carrier-holdase complex: it binds unfolded/hydrophobic protein precursors AND escorts them across the mitochondrial IMS from the TOM complex to the TIM22 complex. GO:0051082 "unfolded protein binding" captures only the binding aspect but misses the essential carrier/escort function. GO:0140309 "unfolded protein holdase activity" was created specifically for this class of proteins (go-ontology#30552) and is the correct replacement term. Reason: TIM9 (as part of the Tim9-Tim10 complex) contributes to a textbook carrier-holdase: it binds unfolded hydrophobic precursor proteins AND escorts them between cellular compartments (principally from TOM to TIM22 across the IMS). GO:0051082 "unfolded protein binding" captures only the binding aspect. GO:0140309 "unfolded protein holdase activity" was created in Nov 2025 specifically for TIM carrier-holdases (go-ontology#30552). The current definition emphasizes binding an unfolded client, escorting it to an acceptor or location, and preventing aggregation. The Tim9-Tim10 complex acts as a chaperone-like protein that protects hydrophobic precursors from aggregation and guides them through the mitochondrial intermembrane space (UniProt). PMID:12138093 shows the reconstituted complex is functional because it binds AAC and displays chaperone activity. Proposed replacements: unfolded protein holdase activity Supporting Evidence: PMID:12138093 the reconstituted TIM10 complex is functional because it bound to the physiological substrate ADP/ATP carrier and displayed chaperone activity in refolding the model substrate firefly luciferase. PMID:9822593 Tim9p is a new subunit of the TIM machinery that guides hydrophobic inner membrane proteins across the aqueous intermembrane space. PMID:9889188 The TIM9.10 complex is more abundant than the TIM9.10.12 complex and mediates partial translocation of mitochondrial carriers proteins across the outer membrane. PMID:10469659 the two 70 kDa complexes each mediate the import of a different subset of integral inner membrane proteins and that they can transfer these proteins to one of three different membrane insertion sites UniProt:O74700 Acts as a chaperone-like protein that protects the hydrophobic precursors from aggregation and guide them through the mitochondrial intermembrane space. file:yeast/TIM9/TIM9-deep-research-falcon.md Tim9 acts as a **chaperone/escort factor** that prevents aggregation of hydrophobic precursors in the aqueous IMS and transfers them from **TOM** to **TIM22**. file:yeast/TIM9/TIM9-deep-research-falcon.md TIM9·10 recognizes hydrophobic clients primarily through a **hydrophobic cleft** formed by chaperone helices file:interpro/panther/PTHR13172/PTHR13172-paint.tsv PTHR13172 PTN004407763 GO:0140309 F IBD false SGD:S000007256|UniProtKB:Q9Y5J7 taxon:2759 20260603 |
| GO:0005743 mitochondrial inner membrane | EXP PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | ACCEPT | Summary: Large-scale yeast mitochondrial proteomics found TIM9 in purified mitochondrial samples; UniProt maps the result to the IMS face of the mitochondrial inner membrane, which is consistent with the low-abundance Tim9 pool bound to the 300 kDa TIM22 inner-membrane complex. Reason: Accept this EXP location row. PMID:16823961 is proteome-scale and abstract-only in the cache, but TIM9 inner-membrane association is independently established by direct TIM22-complex studies, so this row is consistent with the curated biology. Supporting Evidence: PMID:16823961 A total of 851 different proteins (PROMITO dataset) were identified by use of multidimensional LC-MS/MS, 1D-SDS-PAGE combined with nano-LC-MS/MS and 2D-PAGE with subsequent MALDI-mass fingerprinting. PMID:9822593 A small fraction of Tim9p is bound to the outer face of the inner membrane in a 300 kDa complex whose other subunits include Tim54p, Tim22p, Tim12p and Tim10p. |
| GO:0005758 mitochondrial intermembrane space | EXP PMID:22984289 Intermembrane space proteome of yeast mitochondria. | ACCEPT | Summary: The 2012 yeast IMS proteome used Tim9 as a known IMS marker in import assays and independently profiled Bax-releasable IMS proteins from isolated yeast mitochondria. Reason: TIM9 is a canonical IMS small-Tim protein, and this large-scale subcompartment proteomics row is consistent with direct Tim9 localization and complex-assembly evidence. Supporting Evidence: PMID:22984289 the IMS model substrate [35S]Tim9 is imported into a Prot. K protected location independently of Δψ |
| GO:0042719 mitochondrial intermembrane space chaperone complex | IBA GO_REF:0000033 | ACCEPT | Summary: Current PAINT places mitochondrial IMS chaperone-complex membership at the Tim9/TIMM9/TIMM10B ancestral node PTN004407763, and that placement is concordant with direct yeast Tim9-Tim10 heterohexamer evidence. Reason: The IBA is current in the refreshed PTHR13172 PAINT snapshot and transfers the core conserved small-Tim complex location from PTN004407763. The target's own TIM9 experimental evidence is among the descendant evidence behind the node placement; that is valid grounding for PAINT, not a circular source. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN004407763 · Tim9/TIMM9/TIMM10B ancestral node SUPPORTS TRANSFER Current PTHR13172 PAINT places GO:0042719 at PTN004407763, the same ancestral node recorded in GOA for yeast TIM9. Supporting Evidence: file:interpro/panther/PTHR13172/PTHR13172-paint.tsv PTHR13172 PTN004407763 GO:0042719 C IBD false MGI:MGI:1353436|SGD:S000007256|UniProtKB:Q9Y5J6|UniProtKB:Q9Y5J7 taxon:2759 20260128 PMID:9822593 Most of Tim9p is associated with Tim10p in a soluble 70 kDa complex. |
| GO:0042719 mitochondrial intermembrane space chaperone complex | IDA PMID:30445040 Structural Basis of Membrane Protein Chaperoning through the... | ACCEPT | Summary: Structural reconstitution of TIM9-TIM10 used the soluble alternating Tim9/Tim10 hexamer to bind unfolded carrier substrates and VDAC beta-hairpin peptides. Reason: PMID:30445040 directly uses yeast Tim9-Tim10 complexes as the IMS chaperone assembly for structural client-binding work, supporting TIM9 as part of GO:0042719. Supporting Evidence: PMID:30445040 High-resolution structures show that the soluble TIM chaperone complexes assemble as alternating circular hexamers formed by three subunits of each Tim9 and Tim10, or Tim8 and Tim13 for the TIM9·10 and TIM8·13 chaperones, respectively |
| GO:0042719 mitochondrial intermembrane space chaperone complex | IPI PMID:19037098 Structural and functional requirements for activity of the T... | ACCEPT | Summary: Baker et al. solved the yeast Tim9-Tim10 hexamer and used mutational analysis to separate Tim9's structural and substrate-trapping contributions. Reason: The paper directly analyzes Tim9 as part of the Tim9-Tim10 hexameric IMS chaperone complex, so the ComplexPortal IPI row is correct. Supporting Evidence: PMID:19037098 we report the structure of the yeast Tim9-Tim10 hexameric assembly determined to 2.5 A |
| GO:0042719 mitochondrial intermembrane space chaperone complex | IPI PMID:9889188 Tim9, a new component of the TIM22.54 translocase in mitocho... | ACCEPT | Summary: Adam et al. independently found Tim9 in Tim9-Tim10 and Tim9-Tim10-Tim12 assemblies in the mitochondrial intermembrane space. Reason: This direct evidence establishes the Tim9-Tim10 IMS chaperone assembly and the related TIM22-associated Tim9-Tim10-Tim12 assembly. Supporting Evidence: PMID:9889188 One complex contains Tim9 and Tim10. The other complex contains Tim9, Tim10 and Tim12 and is tightly associated with Tim22 in the inner membrane. |
| GO:0042721 TIM22 mitochondrial import inner membrane insertion complex | IPI PMID:10648604 Tim18p, a new subunit of the TIM22 complex that mediates ins... | ACCEPT | Summary: ComplexPortal now carries TIM9 as a peripheral subunit of the TIM22-associated inner-membrane insertion complex from the Koehler et al. TIM18/TIM22 study. Reason: The TIM22 holo-complex contains a peripheral Tim9p-Tim10p-Tim12p module on the IMS face of the inner membrane; TIM9 membership in GO:0042721 is therefore correct. Supporting Evidence: PMID:10648604 The TIM22 complex contains the peripheral subunits Tim9p, Tim10p, and Tim12p and the integral membrane subunits Tim22p and Tim54p. |
| GO:0045039 protein insertion into mitochondrial inner membrane | IEA GO_REF:0000117 | ACCEPT | Summary: New ARBA IEA row for the established small-Tim role in insertion of imported carrier precursors into the mitochondrial inner membrane. Reason: This electronic row is concordant with multiple direct TIM9 experimental rows for carrier import and protein insertion into the mitochondrial inner membrane. Supporting Evidence: UniProt:O74700 Mitochondrial intermembrane chaperone that participates in the import and insertion of multi-pass transmembrane proteins into the mitochondrial inner membrane. |
| GO:0070013 intracellular organelle lumen | IEA GO_REF:0000117 | MODIFY | Summary: ARBA now maps TIM9 to the very broad parent location intracellular organelle lumen, which is biologically true only through the specific mitochondrial intermembrane space localization. Reason: TIM9 is an IMS protein, and GO:0070013 is an overly generic ancestor that loses the mitochondrial specificity established by direct and UniProt evidence. Use GO:0005758 mitochondrial intermembrane space instead. Proposed replacements: mitochondrial intermembrane space Supporting Evidence: UniProt:O74700 Mitochondrion intermembrane space |
| GO:0140309 unfolded protein holdase activity | IDA PMID:30445040 Structural Basis of Membrane Protein Chaperoning through the... | ACCEPT | Summary: Weinhaupl et al. reconstituted TIM9-TIM10 with unfolded carrier precursors and found that the chaperone keeps aggregation-prone carrier substrates soluble and binds them in an elongated translocation-competent state. Reason: This is direct biochemical/structural evidence for GO:0140309; the Tim9-Tim10 complex binds unfolded hydrophobic membrane-protein clients and prevents their aggregation during IMS transit. Supporting Evidence: PMID:30445040 These findings establish that recombinant TIM9·10 is able to bind the precursor proteins in an unfolded form as well as polypeptide exiting the ribosome. |
| GO:0140309 unfolded protein holdase activity | IDA PMID:9822593 Tim9p, an essential partner subunit of Tim10p for the import... | ACCEPT | Summary: Koehler et al. showed that Tim9p is a Tim10p partner in the soluble small-Tim carrier complex and can be cross-linked to a partly translocated carrier precursor. Reason: The carrier-crosslinking and soluble Tim9-Tim10 complex data support TIM9's role in the IMS holdase complex that binds and shields hydrophobic precursor proteins. Supporting Evidence: PMID:9822593 Tim9p can be cross-linked to a partly translocated carrier protein. |
| GO:0140309 unfolded protein holdase activity | IGI PMID:9822593 Tim9p, an essential partner subunit of Tim10p for the import... | ACCEPT | Summary: Koehler et al. found that Tim9p Ser67Cys suppresses tim10-1 and tim12-1 temperature-sensitive phenotypes, genetically connecting Tim9 to the Tim9-Tim10/TIM22 carrier-import pathway. Reason: Suppression of TIM10 and TIM12 mutant phenotypes by a TIM9 allele supports TIM9 activity in the functional IMS holdase and TIM22 handoff system. Supporting Evidence: PMID:9822593 A Ser67-->Cys67 mutation in Tim9p suppresses the temperature-sensitive growth defect of tim10-1 and tim12-1 mutants. |
| GO:7770061 TOM-TIM22-mediated mitochondrial inner membrane protein insertion | IPI PMID:30445040 Structural Basis of Membrane Protein Chaperoning through the... | ACCEPT | Summary: Weinhaupl et al. structurally and genetically analyzed the Tim9-Tim10 complex as the IMS chaperone that receives carrier precursors from TOM and delivers them to the TIM22 carrier-insertion pathway. Reason: GO:7770061 is the new precise child of GO:0045039 for the carrier route that TIM9 executes as part of the small-Tim holdase complex. The PMID:30445040 structural and mutational data directly support Tim9-Tim10 client binding and TIM22 carrier biogenesis. Supporting Evidence: PMID:30445040 The TIM chaperone system is crucial to mediate the transfer of some of the most abundant mitochondrial membrane protein precursors from the TOM complex to either SAM or the TIM22 complexes |
| GO:7770063 beta barrel protein insertion into mitochondrial outer membrane | IPI PMID:30445040 Structural Basis of Membrane Protein Chaperoning through the... | KEEP AS NON CORE | Summary: The 2018 structural study showed that Tim9-Tim10 can engage beta-hairpin VDAC/Por1-derived client peptides and that small-Tim binding-cleft mutants impair beta-barrel protein biogenesis. Reason: TIM9-TIM10 contributes to beta-barrel precursor handling toward SAM, and the direct Por1/VDAC evidence supports this process. The carrier/TIM22 insertion route remains the dominant TIM9 role in the yeast literature, so keep this newer outer-membrane beta-barrel process as a secondary function. Supporting Evidence: PMID:30445040 Mutations in these binding sites cause cell death or growth defects associated with impairment of carrier and β-barrel protein biogenesis. |
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Download this section (compressed HTML)Q: What proportion of TIM9 client handling is directed to TIM22 versus SAM in vivo, and which individual beta-barrel precursors require the Tim9-Tim10 complex?
Q: How do Tim9's structural contribution to the heterohexamer and Tim10's stronger isolated AAC-binding capacity partition client recognition within the intact complex?
Experiment: Perform time-resolved crosslinking of endogenous Tim9 and Tim10 during synchronized import of carrier and beta-barrel precursor panels, quantifying handoff to TIM22 or SAM.
Hypothesis: Tim9-Tim10 directly handles both client classes, but TIM22-directed carrier delivery is the dominant and most robust TIM9-dependent route.
Experiment: Reconstitute Tim9-Tim10 complexes carrying interface-preserving Tim9 client-contact mutations and measure complex assembly, aggregation suppression, and precursor delivery.
Hypothesis: Tim9 contributes client-contact surfaces beyond its structural role, even though isolated Tim10 shows stronger AAC binding than isolated Tim9.
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Download this section (compressed HTML)Essential protein of the mitochondrial intermembrane space; forms a complex with Tim10p (TIM10 complex) that delivers hydrophobic proteins to the TIM22 complex for insertion into the inner membrane
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