6t9k: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
No edit summary
No edit summary
 
Line 3: Line 3:
<SX load='6t9k' size='340' side='right' viewer='molstar' caption='[[6t9k]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
<SX load='6t9k' size='340' side='right' viewer='molstar' caption='[[6t9k]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6t9k]] is a 11 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast] and [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_s288c Saccharomyces cerevisiae s288c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T9K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6T9K FirstGlance]. <br>
<table><tr><td colspan='2'>[[6t9k]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T9K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6T9K FirstGlance]. <br>
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6t9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t9k OCA], [http://pdbe.org/6t9k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6t9k RCSB], [http://www.ebi.ac.uk/pdbsum/6t9k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6t9k ProSAT]</span></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.3&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6t9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t9k OCA], [https://pdbe.org/6t9k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6t9k RCSB], [https://www.ebi.ac.uk/pdbsum/6t9k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6t9k ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/TAF10_YEAST TAF10_YEAST]] Functions as a component of the DNA-binding general transcription factor complex TFIID and the transcription regulatory histone acetylation (HAT) complexes SAGA and SLIK. Binding of TFIID to a promoter (with or without TATA element) is the initial step in preinitiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation by TAF1), facilitation of DNA opening and initiation of transcription. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus.<ref>PMID:10026213</ref> <ref>PMID:10788514</ref> <ref>PMID:11238921</ref> <ref>PMID:11295558</ref> <ref>PMID:12052880</ref> <ref>PMID:12138208</ref> <ref>PMID:12516863</ref> <ref>PMID:9674426</ref> <ref>PMID:9695952</ref>  [[http://www.uniprot.org/uniprot/TAF5_YEAST TAF5_YEAST]] Functions as a component of the DNA-binding general transcription factor complex TFIID and the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and SLIK. Binding of TFIID to a promoter (with or without TATA element) is the initial step in preinitiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation by TAF1), facilitation of DNA opening and initiation of transcription. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA, an altered form of SAGA, may be involved in positive transcriptional regulation. SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus.<ref>PMID:10026213</ref> <ref>PMID:10788514</ref> <ref>PMID:12052880</ref> <ref>PMID:12138208</ref> <ref>PMID:12516863</ref> <ref>PMID:9674426</ref>  [[http://www.uniprot.org/uniprot/HFI1_YEAST HFI1_YEAST]] Functions as component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and SLIK. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA, an altered form of SAGA, may be involved in positive transcriptional regulation. SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. HFI1/ADA1 and SPT20/ADA5 may recruit TATA binding protein (TBP) and possibly other basal factors to bind to the TATA box.<ref>PMID:10026213</ref>  [[http://www.uniprot.org/uniprot/SPT7_YEAST SPT7_YEAST]] Functions as component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and SLIK. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA an altered form of SAGA, may be involved in positive transcriptional regulation. SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. SPT7 is transcriptional activator of TY elements and other genes.<ref>PMID:10026213</ref>  [[http://www.uniprot.org/uniprot/SPT3_YEAST SPT3_YEAST]] Functions as component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and SLIK. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA, an altered form of SAGA, may be involved in positive transcriptional regulation. SPT3 is required for recruitment of TATA-binding protein (TBP) to SAGA-dependent promoters. During SAGA-mediated transcriptional inhibition, SPT3 and SPT8 prevent binding of TBP to the TATA box. SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. SPT factors 3, 7 and 8 are required for the initiation of Ty transcription from the delta promoter. SPT3 regulates Ty1 as well as the mating factor genes.<ref>PMID:10026213</ref> <ref>PMID:10580001</ref> <ref>PMID:10611242</ref> <ref>PMID:11485989</ref> <ref>PMID:12370284</ref>  [[http://www.uniprot.org/uniprot/TAF12_YEAST TAF12_YEAST]] Functions as a component of the DNA-binding general transcription factor complex TFIID and the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and SLIK. Binding of TFIID to a promoter (with or without TATA element) is the initial step in preinitiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation by TAF1), facilitation of DNA opening and initiation of transcription. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA, an altered form of SAGA, may be involved in positive transcriptional regulation. SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus.<ref>PMID:10026213</ref> <ref>PMID:10788514</ref> <ref>PMID:11238921</ref> <ref>PMID:11295558</ref> <ref>PMID:11473260</ref> <ref>PMID:12052880</ref> <ref>PMID:12138208</ref> <ref>PMID:12516863</ref> <ref>PMID:9674426</ref> <ref>PMID:9695952</ref>  [[http://www.uniprot.org/uniprot/SPT20_YEAST SPT20_YEAST]] Transcription regulator. May recruit TATA binding protein (TBP) and possibly other basal factors to bind to the TATA box. Functions as component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and SLIK. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA, an altered form of SAGA, may be involved in positive transcriptional regulation. SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus.<ref>PMID:10026213</ref> [[http://www.uniprot.org/uniprot/TAF6_YEAST TAF6_YEAST]] Functions as a component of the DNA-binding general transcription factor complex TFIID and the regulatory transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and SLIK. Binding of TFIID to a promoter (with or without TATA element) is the initial step in preinitiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation by TAF1), facilitation of DNA opening and initiation of transcription. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA, an altered form of SAGA, may be involved in positive transcriptional regulation. SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus.<ref>PMID:10026213</ref> <ref>PMID:10788514</ref> <ref>PMID:11238921</ref> <ref>PMID:11295558</ref> <ref>PMID:11473260</ref> <ref>PMID:12052880</ref> <ref>PMID:12138208</ref> <ref>PMID:12516863</ref> <ref>PMID:9674426</ref> <ref>PMID:9695952</ref>  [[http://www.uniprot.org/uniprot/SGF73_YEAST SGF73_YEAST]] Functions as component of the transcription regulatory histone acetylation (HAT) complex SAGA. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). [[http://www.uniprot.org/uniprot/TAF9_YEAST TAF9_YEAST]] Functions as a component of the DNA-binding general transcription factor complex TFIID and the transcription regulatory histone acetylation (HAT) complex SAGA and SLIK. Binding of TFIID to a promoter (with or without TATA element) is the initial step in preinitiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation by TAF1), facilitation of DNA opening and initiation of transcription. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3, and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus.<ref>PMID:10026213</ref> <ref>PMID:10788514</ref> <ref>PMID:11238921</ref> <ref>PMID:11295558</ref> <ref>PMID:11473260</ref> <ref>PMID:12052880</ref> <ref>PMID:12138208</ref> <ref>PMID:12516863</ref> <ref>PMID:9674426</ref> <ref>PMID:9695952</ref> 
[https://www.uniprot.org/uniprot/SPT20_YEAST SPT20_YEAST] Transcription regulator. May recruit TATA binding protein (TBP) and possibly other basal factors to bind to the TATA box. Functions as component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and SLIK. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA, an altered form of SAGA, may be involved in positive transcriptional regulation. SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus.<ref>PMID:10026213</ref>  
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
Line 19: Line 20:


==See Also==
==See Also==
*[[SAGA-associated factor|SAGA-associated factor]]
*[[Transcription initiation factors 3D structures|Transcription initiation factors 3D structures]]
*[[Transcription initiation factors 3D structures|Transcription initiation factors 3D structures]]
*[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]]
*[[Transcriptional activator 3D structures|Transcriptional activator 3D structures]]
Line 25: Line 27:
__TOC__
__TOC__
</SX>
</SX>
[[Category: Baker's yeast]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae s288c]]
[[Category: Saccharomyces cerevisiae S288C]]
[[Category: Cheung, A]]
[[Category: Cheung A]]
[[Category: Cramer, P]]
[[Category: Cramer P]]
[[Category: Wang, H]]
[[Category: Wang H]]
[[Category: Coactivator]]
[[Category: Gene regulation]]
[[Category: Histone acetyltransferase]]
[[Category: Histone deubiquitinase]]
[[Category: Transcription]]

Latest revision as of 13:17, 22 May 2024

SAGA Core moduleSAGA Core module

6t9k, resolution 3.30Å

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA