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Yorodumi- PDB-7kts: Negative stain EM structure of the human SAGA coactivator complex... -
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-Basic information
Entry | Database: PDB / ID: 7kts | |||||||||||||||||||||
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Title | Negative stain EM structure of the human SAGA coactivator complex (TRRAP, core, splicing module) | |||||||||||||||||||||
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Keywords | TRANSCRIPTION / splicing / gene regulation / chromatin | |||||||||||||||||||||
Function / homology | Function and homology information SAGA-type complex / positive regulation of response to stimulus / regulation of somatic stem cell population maintenance / regulation of cellular response to stress / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / transcription factor TFTC complex / SLIK (SAGA-like) complex / splicing factor binding ...SAGA-type complex / positive regulation of response to stimulus / regulation of somatic stem cell population maintenance / regulation of cellular response to stress / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / transcription factor TFTC complex / SLIK (SAGA-like) complex / splicing factor binding / U12-type spliceosomal complex / negative regulation of microtubule depolymerization / hepatocyte differentiation / maintenance of protein location in nucleus / RNA splicing, via transesterification reactions / U2-type spliceosomal complex / U2-type precatalytic spliceosome / U2-type prespliceosome assembly / RNA polymerase binding / SAGA complex / U2 snRNP / limb development / transcription preinitiation complex / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / NuA4 histone acetyltransferase complex / precatalytic spliceosome / nucleus organization / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / mRNA Splicing - Minor Pathway / regulation of RNA splicing / histone deacetylase complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / histone acetyltransferase complex / embryonic placenta development / positive regulation of transcription initiation by RNA polymerase II / U2 snRNA binding / regulation of DNA repair / somitogenesis / RNA polymerase II preinitiation complex assembly / gastrulation / RNA Polymerase II Pre-transcription Events / visual perception / TBP-class protein binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / male germ cell nucleus / DNA-templated transcription initiation / promoter-specific chromatin binding / nuclear estrogen receptor binding / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / spliceosomal complex / mRNA transcription by RNA polymerase II / multicellular organism growth / negative regulation of protein catabolic process / autophagy / nuclear matrix / cytoplasmic ribonucleoprotein granule / mRNA splicing, via spliceosome / microtubule cytoskeleton organization / G1/S transition of mitotic cell cycle / transcription corepressor activity / microtubule cytoskeleton / HATs acetylate histones / positive regulation of cell growth / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / transcription coactivator activity / protein stabilization / Ub-specific processing proteases / nuclear speck / chromatin remodeling / protein heterodimerization activity / DNA repair / focal adhesion / apoptotic process / protein-containing complex binding / regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) unclassified Rhodococcus (bacteria) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 19.09 Å | |||||||||||||||||||||
Authors | Herbst, D.A. / Esbin, M.N. / Nogales, E. | |||||||||||||||||||||
Funding support | United States, European Union, Switzerland, 6items
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Citation | Journal: Nat Struct Mol Biol / Year: 2021 Title: Structure of the human SAGA coactivator complex. Authors: Dominik A Herbst / Meagan N Esbin / Robert K Louder / Claire Dugast-Darzacq / Gina M Dailey / Qianglin Fang / Xavier Darzacq / Robert Tjian / Eva Nogales / Abstract: The SAGA complex is a regulatory hub involved in gene regulation, chromatin modification, DNA damage repair and signaling. While structures of yeast SAGA (ySAGA) have been reported, there are ...The SAGA complex is a regulatory hub involved in gene regulation, chromatin modification, DNA damage repair and signaling. While structures of yeast SAGA (ySAGA) have been reported, there are noteworthy functional and compositional differences for this complex in metazoans. Here we present the cryogenic-electron microscopy (cryo-EM) structure of human SAGA (hSAGA) and show how the arrangement of distinct structural elements results in a globally divergent organization from that of yeast, with a different interface tethering the core module to the TRRAP subunit, resulting in a dramatically altered geometry of functional elements and with the integration of a metazoan-specific splicing module. Our hSAGA structure reveals the presence of an inositol hexakisphosphate (InsP) binding site in TRRAP and an unusual property of its pseudo-(Ψ)PIKK. Finally, we map human disease mutations, thus providing the needed framework for structure-guided drug design of this important therapeutic target for human developmental diseases and cancer. | |||||||||||||||||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 7kts.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7kts.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7kts.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kts_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7kts_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7kts_validation.xml.gz | 154.7 KB | Display | |
Data in CIF | 7kts_validation.cif.gz | 246.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/7kts ftp://data.pdbj.org/pub/pdb/validation_reports/kt/7kts | HTTPS FTP |
-Related structure data
Related structure data | 23028MC 7ktrC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
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-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 8 types, 8 molecules ABCDFIJN
#1: Protein | Mass: 419168.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: F2Z2U4 |
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#2: Protein | Mass: 66223.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75529 |
#3: Protein | Mass: 88129.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NEM7 |
#4: Protein | Mass: 83013.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) unclassified Rhodococcus (bacteria) Gene: SUPT7L, KIAA0764 / Production host: Homo sapiens (human) / References: UniProt: O94864 |
#6: Protein | Mass: 62027.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y6J9 |
#9: Protein | Mass: 35447.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75486 |
#10: Protein | Mass: 37432.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96BN2 |
#11: Protein | Mass: 95597.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15265 |
-Transcription initiation factor TFIID subunit ... , 3 types, 3 molecules EGH
#5: Protein | Mass: 27654.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9HBM6 |
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#7: Protein | Mass: 17948.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16514 |
#8: Protein | Mass: 21731.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q12962 |
-Splicing factor 3B subunit ... , 2 types, 2 molecules ST
#12: Protein | Mass: 135718.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15393 |
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#13: Protein | Mass: 10149.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BWJ5 |
-Details
Sequence details | Portions of chains A, D, F and I were not fully discernible in the map, and so many of the residues ...Portions of chains A, D, F and I were not fully discernible in the map, and so many of the residues were modeled as unknown (UNK) due to not knowing the register in these regions. The full sequence of the chains are as follows. Chain A: MAFVATQGAT |
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