[English] 日本語
Yorodumi- PDB-7ktr: Cryo-EM structure of the human SAGA coactivator complex (TRRAP, core) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ktr | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the human SAGA coactivator complex (TRRAP, core) | |||||||||||||||||||||
Components |
| |||||||||||||||||||||
Keywords | TRANSCRIPTION / coactivator / gene regulation / chromatin | |||||||||||||||||||||
Function / homology | Function and homology information SAGA-type complex / regulation of primary metabolic process / 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 / negative regulation of microtubule depolymerization ...SAGA-type complex / regulation of primary metabolic process / 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 / negative regulation of microtubule depolymerization / hepatocyte differentiation / maintenance of protein location in nucleus / RNA polymerase binding / limb development / SAGA complex / transcription preinitiation complex / embryonic placenta development / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 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 / regulation of RNA splicing / histone deacetylase complex / histone acetyltransferase complex / positive regulation of transcription initiation by RNA polymerase II / male germ cell nucleus / somitogenesis / regulation of DNA repair / RNA polymerase II preinitiation complex assembly / transcription coregulator activity / gastrulation / RNA Polymerase II Pre-transcription Events / visual perception / TBP-class protein binding / DNA-templated transcription initiation / mRNA transcription by RNA polymerase II / promoter-specific chromatin binding / nuclear estrogen receptor binding / transcription initiation at RNA polymerase II promoter / multicellular organism growth / G1/S transition of mitotic cell cycle / nuclear matrix / microtubule cytoskeleton organization / autophagy / cytoplasmic ribonucleoprotein granule / transcription corepressor activity / microtubule cytoskeleton / positive regulation of cell growth / HATs acetylate histones / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / transcription coactivator activity / transcription by RNA polymerase II / chromatin remodeling / protein stabilization / Ub-specific processing proteases / nuclear speck / protein heterodimerization activity / focal adhesion / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of apoptotic process / regulation of DNA-templated transcription / nucleolus / apoptotic process / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) unclassified Rhodococcus (bacteria) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å | |||||||||||||||||||||
Authors | Herbst, D.A. / Esbin, M.N. / Nogales, E. | |||||||||||||||||||||
Funding support | United States, European Union, Switzerland, 6items
| |||||||||||||||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ktr.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ktr.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 7ktr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ktr_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7ktr_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7ktr_validation.xml.gz | 131.5 KB | Display | |
Data in CIF | 7ktr_validation.cif.gz | 205.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/7ktr ftp://data.pdbj.org/pub/pdb/validation_reports/kt/7ktr | HTTPS FTP |
-Related structure data
Related structure data | 23027MC 7ktsC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 8 types, 8 molecules ABCDFIJN
#1: Protein | Mass: 353170.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HeLa / References: UniProt: F2Z2U4 |
---|---|
#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: 78079.922 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: 67903.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y6J9 |
#9: Protein | Mass: 33197.047 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 |
---|---|
#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 |
-Non-polymers , 1 types, 1 molecules
#12: Chemical | ChemComp-IHP / |
---|
-Details
Has ligand of interest | Y |
---|---|
Sequence details | Portions of chains A, D and I were not fully discernible in the map, and so many of the residues ...Portions of chains A, D 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 |