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Yorodumi- PDB-7vdt: The motor-nucleosome module of human chromatin remodeling PBAF-nu... -
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-Basic information
Entry | Database: PDB / ID: 7vdt | ||||||
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Title | The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / complex | ||||||
Function / homology | Function and homology information positive regulation of glucose mediated signaling pathway / bBAF complex / npBAF complex / nBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of androgen receptor signaling pathway / neural retina development / GBAF complex / regulation of G0 to G1 transition / Tat protein binding ...positive regulation of glucose mediated signaling pathway / bBAF complex / npBAF complex / nBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of androgen receptor signaling pathway / neural retina development / GBAF complex / regulation of G0 to G1 transition / Tat protein binding / nucleosome disassembly / EGR2 and SOX10-mediated initiation of Schwann cell myelination / regulation of nucleotide-excision repair / RSC-type complex / RNA polymerase I preinitiation complex assembly / positive regulation by host of viral transcription / SWI/SNF complex / ATP-dependent chromatin remodeler activity / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear androgen receptor binding / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / positive regulation of Wnt signaling pathway / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / Chromatin modifying enzymes / DNA polymerase binding / transcription initiation-coupled chromatin remodeling / Interleukin-7 signaling / helicase activity / transcription coregulator binding / positive regulation of cell differentiation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Formation of the beta-catenin:TCF transactivating complex / lysine-acetylated histone binding / negative regulation of cell growth / kinetochore / fibrillar center / RMTs methylate histone arginines / nuclear matrix / positive regulation of miRNA transcription / structural constituent of chromatin / transcription corepressor activity / positive regulation of DNA-binding transcription factor activity / nucleosome / p53 binding / nervous system development / positive regulation of cold-induced thermogenesis / transcription coactivator activity / hydrolase activity / chromatin remodeling / protein heterodimerization activity / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular space / RNA binding / nucleoplasm / ATP binding / membrane / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Xenopus laevis (African clawed frog) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Chen, Z.C. / Chen, K.J. / Yuan, J.J. | ||||||
Funding support | China, 1items
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Citation | Journal: Nature / Year: 2022 Title: Structure of human chromatin-remodelling PBAF complex bound to a nucleosome. Authors: Junjie Yuan / Kangjing Chen / Wenbo Zhang / Zhucheng Chen / Abstract: DNA wraps around the histone octamer to form nucleosomes, the repeating unit of chromatin, which create barriers for accessing genetic information. Snf2-like chromatin remodellers couple the energy ...DNA wraps around the histone octamer to form nucleosomes, the repeating unit of chromatin, which create barriers for accessing genetic information. Snf2-like chromatin remodellers couple the energy of ATP binding and hydrolysis to reposition and recompose the nucleosome, and have vital roles in various chromatin-based transactions. Here we report the cryo-electron microscopy structure of the 12-subunit human chromatin-remodelling polybromo-associated BRG1-associated factor (PBAF) complex bound to the nucleosome. The motor subunit SMARCA4 engages the nucleosome in the active conformation, which reveals clustering of multiple disease-associated mutations at the interfaces that are essential for chromatin-remodelling activity. SMARCA4 recognizes the H2A-H2B acidic pocket of the nucleosome through three arginine anchors of the Snf2 ATP coupling (SnAc) domain. PBAF shows notable functional modularity, and most of the auxiliary subunits are interwoven into three lobe-like submodules for nucleosome recognition. The PBAF-specific auxiliary subunit ARID2 acts as the structural core for assembly of the DNA-binding lobe, whereas PBRM1, PHF10 and BRD7 are collectively incorporated into the lobe for histone tail binding. Together, our findings provide mechanistic insights into nucleosome recognition by PBAF and a structural basis for understanding SMARCA4-related human diseases. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vdt.cif.gz | 407 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vdt.ent.gz | 309.5 KB | Display | PDB format |
PDBx/mmJSON format | 7vdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/7vdt ftp://data.pdbj.org/pub/pdb/validation_reports/vd/7vdt | HTTPS FTP |
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-Related structure data
Related structure data | 31925MC 7vdvC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 5 types, 9 molecules ABFCGDHEK
#1: Protein | Mass: 169597.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4, BAF190A, BRG1, SNF2B, SNF2L4 / Production host: Homo sapiens (human) References: UniProt: P51532, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement | ||||||
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#2: Protein | Mass: 11394.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799 #3: Protein | Mass: 14109.436 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591, XELAEV_18003602mg / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8 #4: Protein | Mass: 13965.265 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281 #5: Protein | Mass: 15435.126 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18002543mg / Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1 |
-DNA chain , 2 types, 2 molecules IJ
#6: DNA chain | Mass: 63679.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#7: DNA chain | Mass: 64145.816 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 3 molecules
#8: Chemical | ChemComp-BEF / |
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#9: Chemical | ChemComp-MG / |
#10: Chemical | ChemComp-ADP / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex Type: COMPLEX / Entity ID: #1-#7 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 208905 / Symmetry type: POINT |