POB3 is the small subunit of the FACT (Facilitates Chromatin Transcription) complex, an essential heterodimeric histone chaperone that works with Spt16 to dynamically reorganize nucleosomes during transcription elongation, DNA replication, and DNA repair. Unlike mammalian SSRP1, yeast POB3 lacks intrinsic DNA-binding capacity and instead cooperates with Nhp6 proteins for DNA recognition. POB3 specifically binds H2A-H2B dimers through its acidic C-terminus and contributes to H3-H4 interactions through its middle pleckstrin homology domains. The protein is essential for cell viability and localizes to active transcription sites and replication forks within chromatin.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0035101 FACT complex | IBA GO_REF:0000033 | ACCEPT | Summary: POB3 is an integral, obligate component of the FACT complex. IBA evidence from phylogenetic analysis is appropriate given the conserved role of POB3/SSRP1 orthologs across eukaryotes. This annotation correctly identifies POB3's core cellular role as a structural component of the FACT heterodimer. Reason: POB3 is the second essential subunit of FACT, functioning obligately with Spt16. The IBA code reflects proper phylogenetic inference of this fundamental complex membership. This is core function. Supporting Evidence: PMID:9705338 Characterization of the CP complex, an abundant dimer of Cdc68 and Pob3 proteins file:yeast/POB3/POB3-deep-research-perplexity.md provider: perplexity file:yeast/POB3/POB3-deep-research-falcon.md In budding yeast, FACT is built around an essential Spt16βPob3 heterodimer and functions together with HMGB proteins (notably Nhp6) to engage nucleosomes during chromatin-based processes. |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | REMOVE | Summary: IEA annotation based on InterPro domain IPR000969 (SSRP1/POB3). However, this annotation is misleading in the context of yeast POB3. While POB3 contains domains shared with SSRP1 family members, POB3 itself lacks intrinsic DNA-binding capacity. DNA binding in the yeast FACT complex is provided by Nhp6 proteins, not POB3. The domain annotation is correct at the sequence level but does not reflect actual POB3 function. Reason: Yeast POB3 does not directly bind DNA. Unlike mammalian SSRP1 which contains an HMG-box domain for DNA binding, POB3 achieves FACT function through cooperation with Nhp6 proteins that provide DNA-binding capability. UniProt itself notes: 'In contrast to the orthologous protein in animals and plants, this protein does not contain a HMG box DNA-binding domain. This function may instead be provided by the HMG box of the associated NHP6A/NHP6B proteins in the FACT complex of yeast.' IEA propagation of mammalian annotations to yeast is inappropriate. Supporting Evidence: PMID:11432837 Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucleosome-binding factor SPN UniProt:Q04636 In contrast to the orthologous protein in animals and plants, this protein does not contain a HMG box DNA-binding domain. This function may instead be provided by the HMG box of the associated NHP6A/NHP6B proteins file:yeast/POB3/POB3-deep-research-falcon.md FACT comprises Spt16 and Pob3 as core subunits, with Nhp6 providing an HMGB DNA-binding module that cooperates with the Spt16βPob3 core to bind/reorganize nucleosomes (often described as an SPN-like nucleosome-binding assembly). |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: POB3 is a nuclear protein that localizes to the nucleus and associates with chromatin. This IEA annotation based on InterPro domain inference is correct. POB3 is exclusively nuclear in function. Reason: POB3 is functionally restricted to the nucleus where it participates in transcription, replication, and DNA repair. Multiple studies confirm nuclear localization and chromatin association. Supporting Evidence: PMID:10413469 Spt16 and Pob3 of Saccharomyces cerevisiae form an essential, abundant heterodimer that is nuclear, chromatin-associated, and copurifies with DNA polymerase alpha file:yeast/POB3/POB3-deep-research-falcon.md A monopartite C-terminal NLS was mapped to Pob3 residues 544β552 (sequence **RPSKKPKVE**, NLS score **9.5/10**). Deleting this segment (Ξ544β552) or mutating key residues (e.g., K547M) disrupts nuclear localization of Pob3-GFP fusions. |
| GO:0005694 chromosome | IEA GO_REF:0000044 | ACCEPT | Summary: POB3 associates with chromosomal DNA through its interaction with nucleosomes and chromatin. IEA annotation from UniProt subcellular location mapping is supported by direct experimental evidence. Reason: POB3 functions in chromatin organization and nucleosome dynamics on chromosomal DNA. The association is fundamental to its role in transcription, replication, and repair. Supporting Evidence: PMID:10413469 chromatin-associated |
| GO:0006260 DNA replication | IEA GO_REF:0000043 | ACCEPT | Summary: This IEA annotation infers POB3 involvement in DNA replication from UniProt keyword mapping. This is well-supported by experimental evidence for FACT's critical role in replication-coupled nucleosome assembly and fork progression. Reason: POB3 is essential for DNA replication fork progression and replication-coupled chromatin assembly. The term is appropriately general; more specific BP terms exist but this broad term is accurate. Supporting Evidence: PMID:10924459 POB3 is required for both transcription and replication in the yeast Saccharomyces cerevisiae file:yeast/POB3/POB3-deep-research-falcon.md The Pob3 acidic CTD contributes to replication-linked functions: CTD deletion (ΞS491βE543) yields hydroxyurea sensitivity, supporting a role in DNA replication/replication stress responses. |
| GO:0006281 DNA repair | IEA GO_REF:0000043 | ACCEPT | Summary: IEA inference of POB3's role in DNA repair from UniProt keyword. FACT contributes to DNA repair by facilitating chromatin remodeling during nucleotide excision repair (NER) and other pathways that require nucleosome dynamics. Reason: POB3 participates in DNA repair through FACT-mediated nucleosome reorganization that exposes lesions and permits repair protein access. The term is appropriately general. Supporting Evidence: UniProt:Q04636 the FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication and DNA repair |
| GO:0006351 DNA-templated transcription | IEA GO_REF:0000043 | KEEP AS NON CORE | Summary: This broad IEA term is supported by extensive literature on FACT's role as an RNA polymerase II elongation factor. However, a more specific term exists and is already annotated (see GO:0006261 DNA-templated DNA replication). Reason: While technically accurate, this term is too general for POB3's primary transcription role. POB3's specific function is in transcription elongation, not initiation or general transcription. The more specific role in RNA Pol II elongation is captured in other annotations. Can be kept but is less informative than specific elongation terms. Supporting Evidence: PMID:15987999 The yeast FACT complex has a role in transcriptional initiation file:yeast/POB3/POB3-deep-research-falcon.md Mutations affecting FACT subunits are associated with cryptic transcription initiation within gene bodies and altered chromatin states, consistent with a key role for FACT/Pob3 in restoring or maintaining nucleosome organization during and after transcription. |
| GO:0006974 DNA damage response | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | Summary: IEA inference of POB3's involvement in DNA damage response from UniProt keywords. However, this is a secondary consequence of POB3's role in DNA repair, not a primary regulatory role in the damage response (sensing, checkpoint control, etc.). Reason: POB3's role in DNA repair processes is a consequence of its nucleosome reorganization activity, not active participation in DNA damage sensing, checkpoint regulation, or transcriptional response to damage. More specific DNA repair terms are more informative. Supporting Evidence: UniProt:Q04636 The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication and DNA repair |
| GO:0005515 protein binding | IPI PMID:11805837 Systematic identification of protein complexes in Saccharomy... | KEEP AS NON CORE | Summary: IPI evidence from mass spectrometry identifying POB3 interactions. While technically correct, 'protein binding' is uninformative per GO curation guidelines. This annotation should be replaced with specific binding functions. Reason: All the IPI protein binding annotations (multiple entries from different PMIDs documenting interactions with Spt16, various transcription and DNA replication factors, histones) reflect real interaction data but lack molecular specificity. Per GO curation guidelines, avoid generic 'protein binding' and use more specific binding terms (e.g., histone binding, which is already annotated). These support the broader functional annotations but should not be core. Supporting Evidence: PMID:11805837 Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry |
| GO:0005515 protein binding | IPI PMID:11927560 The Paf1 complex physically and functionally associates with... | KEEP AS NON CORE | Summary: IPI evidence from proteomics identifying PAF1 complex association with FACT complex Reason: Generic protein binding term. Specific interactions with transcription elongation factors are implied but should use specific binding terms. Supporting Evidence: PMID:11927560 The Paf1 complex physically and functionally associates with transcription elongation factors in vivo |
| GO:0005515 protein binding | IPI PMID:12242279 RNA polymerase II elongation factors of Saccharomyces cerevi... | KEEP AS NON CORE | Summary: IPI evidence from targeted proteomics of RNA Pol II elongation factors identifying POB3 associations. Reason: Generic protein binding annotation from elongation factor proteomics. Histone binding is more specific and already annotated. Supporting Evidence: PMID:12242279 RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach |
| GO:0005515 protein binding | IPI PMID:16299494 A phosphatase complex that dephosphorylates gammaH2AX regula... | KEEP AS NON CORE | Summary: IPI evidence from phosphatase complex interaction study. Reason: Generic protein binding. Specific functional role not established. Supporting Evidence: PMID:16299494 A phosphatase complex that dephosphorylates gammaH2AX |
| GO:0005515 protein binding | IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine... | KEEP AS NON CORE | Summary: IPI evidence from proteome survey of yeast cell machinery modularity. Reason: Generic protein binding from broad proteome analysis. Supporting Evidence: PMID:16429126 Proteome survey reveals modularity of the yeast cell machinery |
| GO:0005515 protein binding | IPI PMID:16554755 Global landscape of protein complexes in the yeast Saccharom... | KEEP AS NON CORE | Summary: IPI evidence from the global landscape of yeast protein complexes, representing large-scale interaction mapping. Reason: Generic protein binding from high-throughput complex mapping. Multiple interactions confirmed but should use specific binding terms for functional annotations. Supporting Evidence: PMID:16554755 Global landscape of protein complexes in the yeast Saccharomyces cerevisiae |
| GO:0005515 protein binding | IPI PMID:16678108 The structure of the yFACT Pob3-M domain, its interaction wi... | KEEP AS NON CORE | Summary: IPI evidence from structural study of Pob3-M domain interaction with RPA1 (replication factor A). This is the most specific of the protein binding annotations, revealing a direct structural interaction relevant to DNA replication. Reason: While this reveals a specific functional interaction with DNA replication machinery, generic 'protein binding' is still less informative than a term specifying the interaction type. However, this is real experimental evidence. Supporting Evidence: PMID:16678108 The structure of the yFACT Pob3-M domain, its interaction with the DNA replication factor RPA, and a potential role in nucleosome deposition |
| GO:0005515 protein binding | IPI PMID:21179020 Defining the budding yeast chromatin-associated interactome. | KEEP AS NON CORE | Summary: IPI evidence from chromatin-associated interactome mapping defining POB3's interaction network. Reason: Generic protein binding from interactome study. Multiple specific interactions identified but term lacks molecular detail. Supporting Evidence: PMID:21179020 Defining the budding yeast chromatin-associated interactome |
| GO:0005515 protein binding | IPI PMID:22198837 Two surfaces on the histone chaperone Rtt106 mediate histone... | KEEP AS NON CORE | Summary: IPI evidence from histone chaperone Rtt106 interaction study mentioning POB3 associations. Reason: Generic protein binding from histone chaperone interaction study. Supporting Evidence: PMID:22198837 Two surfaces on the histone chaperone Rtt106 mediate histone binding, replication, and silencing |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | KEEP AS NON CORE | Summary: IPI evidence from recent comprehensive yeast protein interactome study confirming POB3 participation in multiple protein-protein interactions. Reason: Generic protein binding from large-scale interactome mapping. Confirms multiple interactions but lacks functional specificity. Supporting Evidence: PMID:37968396 The social and structural architecture of the yeast protein interactome |
| GO:0006261 DNA-templated DNA replication | NAS PMID:12952948 Multiple Nhp6 molecules are required to recruit Spt16-Pob3 t... | ACCEPT | Summary: NAS (Noncurated Author Statement) evidence from ComplexPortal annotation based on PMID:12952948 documenting POB3's role in nucleosome reorganization during replication. This is a core function of FACT. Reason: POB3 is essential for replication-coupled nucleosome assembly and fork progression. NAS from complex annotation is appropriate. This is a fundamental biological function. Supporting Evidence: PMID:12952948 Multiple Nhp6 molecules are required to recruit Spt16-Pob3 to form yFACT complexes and to reorganize nucleosomes |
| GO:0034728 nucleosome organization | NAS PMID:12952948 Multiple Nhp6 molecules are required to recruit Spt16-Pob3 t... | ACCEPT | Summary: NAS evidence documenting POB3's central role in nucleosome reorganization. This is a core functional annotation reflecting FACT's primary biochemical activity. Reason: Nucleosome organization is the fundamental mechanism by which POB3 executes its roles in transcription, replication, and repair. This is core function. Supporting Evidence: PMID:12952948 Multiple Nhp6 molecules are required to recruit Spt16-Pob3 to form yFACT complexes and to reorganize nucleosomes |
| GO:1902275 regulation of chromatin organization | NAS PMID:12952948 Multiple Nhp6 molecules are required to recruit Spt16-Pob3 t... | MODIFY | Summary: NAS evidence from ComplexPortal annotation. FACT dynamically reorganizes chromatin structure in response to transcriptional and replicational demands. However, POB3 is not a regulatory protein per se, but rather an executor of nucleosome dynamics. Reason: While POB3 participates in chromatin dynamics, calling it 'regulation of chromatin organization' is semantically imprecise. POB3's histone chaperone activity directly mediates nucleosome disassembly and reassembly, which IS chromatin organization, not regulation of it. The term GO:0006325 'chromatin organization' (already annotated with IDA) is more accurate. GO:1902275 implies POB3 controls or regulates other chromatin-organizing processes, which is not its primary function. Proposed replacements: chromatin organization Supporting Evidence: PMID:12952948 2003 Sep 1. Multiple Nhp6 molecules are required to recruit Spt16-Pob3 to form yFACT complexes and to reorganize nucleosomes. |
| GO:0006325 chromatin organization | IDA PMID:15082784 Structural features of nucleosomes reorganized by yeast FACT... | ACCEPT | Summary: IDA evidence from structural study of nucleosomes reorganized by yeast FACT, directly demonstrating POB3's role in chromatin organization through nucleosome remodeling and restructuring. Reason: This is core function. FACT-mediated nucleosome reorganization IS chromatin organization. IDA evidence from experimental study of FACT nucleosome remodeling is strong. Supporting Evidence: PMID:15082784 Structural features of nucleosomes reorganized by yeast FACT and its HMG box component, Nhp6 |
| GO:0006325 chromatin organization | IDA PMID:19683499 yFACT induces global accessibility of nucleosomal DNA withou... | ACCEPT | Summary: IDA evidence from study showing yFACT induces global accessibility of nucleosomal DNA without H2A-H2B displacement. This demonstrates the distinct mechanism by which POB3/FACT reorganizes chromatin. Reason: IDA evidence from experimental demonstration of chromatin accessibility induced by FACT. This shows POB3 executes chromatin organization through specific nucleosome reorganization mechanisms. Supporting Evidence: PMID:19683499 yFACT induces global accessibility of nucleosomal DNA without H2A-H2B displacement |
| GO:0000785 chromatin | IDA PMID:10413469 Spt16 and Pob3 of Saccharomyces cerevisiae form an essential... | ACCEPT | Summary: IDA evidence for POB3 localization to chromatin. This is a cellular component annotation correctly demonstrating that POB3 localizes to and associates with chromatin structures. Reason: POB3 is a chromatin-associated protein. Direct localization has been demonstrated. This is accurate as a cellular component term. Supporting Evidence: PMID:10413469 chromatin-associated |
| GO:0003682 chromatin binding | IDA PMID:10413469 Spt16 and Pob3 of Saccharomyces cerevisiae form an essential... | ACCEPT | Summary: IDA evidence for POB3's direct binding to chromatin. This molecular function annotation captures POB3's ability to physically interact with nucleosomes and chromatin structures. Reason: POB3 binds chromatin through histone interactions and nucleosome engagement. This is a core molecular function. IDA from biochemical and localization studies is appropriate. Supporting Evidence: PMID:11432837 Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucleosome-binding factor SPN PMID:10413469 Spt16 and Pob3 of Saccharomyces cerevisiae form an essential, abundant heterodimer that is nuclear, chromatin-associated, and copurifies with DNA polymerase alpha. |
| GO:0006261 DNA-templated DNA replication | IMP PMID:10924459 POB3 is required for both transcription and replication in t... | ACCEPT | Summary: IMP (Inferred from Mutant Phenotype) evidence from conditional POB3 mutants showing defects in DNA replication. This is strong genetic evidence for POB3's essential role in replication. Reason: This is core function. IMP evidence from genetic studies directly demonstrates POB3's requirement for DNA replication. Conditional mutants display replication defects. Supporting Evidence: PMID:10924459 POB3 is required for both transcription and replication in the yeast Saccharomyces cerevisiae |
| GO:0006261 DNA-templated DNA replication | IGI PMID:10924459 POB3 is required for both transcription and replication in t... | ACCEPT | Summary: IGI (Inferred from Genetic Interaction) evidence documenting synthetic genetic interactions between pob3 and genes encoding other replication factors, confirming POB3's functional role in replication machinery. Reason: IGI evidence reveals functional genetic interactions supporting POB3's direct involvement in DNA replication through interactions with other replication factors. Core function. Supporting Evidence: PMID:10924459 POB3 is required for both transcription and replication in the yeast |
| GO:0006261 DNA-templated DNA replication | IPI PMID:9199353 The Saccharomyces cerevisiae DNA polymerase alpha catalytic ... | ACCEPT | Summary: IPI evidence from biochemical study showing POB3 physically associates with DNA polymerase alpha, the replication initiation polymerase. This demonstrates direct interaction with replication machinery. Reason: Direct physical interaction with replication polymerase demonstrates POB3's participation in replication. The multiple evidence codes (NAS, IMP, IGI, IPI) for this single term converge on the same core function. Supporting Evidence: PMID:9199353 The Saccharomyces cerevisiae DNA polymerase alpha catalytic subunit interacts with Cdc68/Spt16 and with Pob3 file:yeast/POB3/POB3-deep-research-falcon.md A recent mechanistic proposal (preprint) suggests that FACT can form an H3βH4βmediated bridge to DNA polymerase Ξ± (Pol Ξ±) via Pol1βs N-terminal domain: H3βH4 promotes FACTβPol Ξ± association, and the resulting ternary complex stimulates Pol Ξ± polymerase activity to coordinate lagging-strand synthesis with nucleosome assembly. |
| GO:0031491 nucleosome binding | IDA PMID:11432837 Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucl... | ACCEPT | Summary: IDA evidence from study of the nucleosome-binding factor SPN (Spt16-Pob3-Nhp6). Direct experimental evidence that POB3 binds nucleosomes. Reason: POB3 directly binds nucleosomes through histone interactions. This is a core molecular function. IDA from biochemical characterization is strong evidence. Supporting Evidence: PMID:11432837 Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucleosome-binding factor SPN |
| GO:0035101 FACT complex | IDA PMID:9705338 Characterization of the CP complex, an abundant dimer of Cdc... | ACCEPT | Summary: IDA evidence from characterization study of the CP (Cdc68/POB3) complex showing this is an abundant dimer that regulates transcription and chromatin. Earlier independent confirmation of POB3 as a FACT component. Reason: This is redundant with the IBA annotation of the same term but provides IDA experimental support. POB3 is confirmed as FACT complex component through direct biochemical characterization. IDA is strong evidence. Supporting Evidence: PMID:9705338 Characterization of the CP complex, an abundant dimer of Cdc68 and Pob3 proteins |
| GO:0042393 histone binding | IDA PMID:18089575 Structural and functional analysis of the Spt16p N-terminal ... | ACCEPT | Summary: IDA evidence from structural and functional analysis of Spt16 N-terminal domain showing overlapping roles of FACT subunits in histone binding. POB3 contributes histone binding through multiple domains (middle domain for H3-H4, C-terminal for H2A-H2B). Reason: This is core molecular function. POB3 directly binds histones through its C-terminal acidic region (H2A-H2B binding) and middle pleckstrin homology domains (H3-H4 binding). IDA from biochemical studies is strong. Supporting Evidence: PMID:18089575 Structural and functional analysis of the Spt16p N-terminal domain reveals overlapping roles of yFACT subunits file:yeast/POB3/POB3-deep-research-falcon.md A central mechanistic role for Pob3 is to provide direct histone-binding capacityβespecially to H2AβH2Bβthrough its acidic CTD. In vivo photo-crosslinking identifies multiple Pob3-CTD sites that directly contact H2A/H2B |
| GO:0045899 positive regulation of RNA polymerase II transcription preinitiation complex assembly | IDA PMID:15987999 The yeast FACT complex has a role in transcriptional initiat... | ACCEPT | Summary: IDA evidence demonstrating POB3/FACT role in facilitating transcription initiation. While FACT is primarily known as an elongation factor, evidence shows it promotes preinitiation complex assembly and stabilizes SPT15/TBP binding to TATA boxes. Reason: FACT has documented roles in both transcription initiation and elongation. IDA evidence shows POB3 promotes formation of preinitiation complexes. This is a secondary but confirmed function. Core function is elongation, but this initiation role is documented. Supporting Evidence: PMID:15987999 The yeast FACT complex has a role in transcriptional initiation UniProt:Q04636 promotes SPT15/TBP-binding to a TATA box |
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