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- PDB-7vdv: The overall structure of human chromatin remodeling PBAF-nucleoso... -
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Basic information
Entry | Database: PDB / ID: 7vdv | ||||||
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Title | The overall structure of human chromatin remodeling PBAF-nucleosome complex | ||||||
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![]() | DNA BINDING PROTEIN / complex | ||||||
Function / homology | ![]() single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / regulation of transepithelial transport / morphogenesis of a polarized epithelium / blastocyst hatching ...single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / regulation of transepithelial transport / morphogenesis of a polarized epithelium / blastocyst hatching / bBAF complex / postsynaptic actin cytoskeleton organization / protein localization to adherens junction / postsynaptic actin cytoskeleton / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / npBAF complex / negative regulation of androgen receptor signaling pathway / Tat protein binding / brahma complex / structural constituent of postsynaptic actin cytoskeleton / nBAF complex / GBAF complex / neural retina development / regulation of G0 to G1 transition / dense body / Formation of annular gap junctions / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / EGR2 and SOX10-mediated initiation of Schwann cell myelination / apical protein localization / regulation of double-strand break repair / coronary artery morphogenesis / nucleosome disassembly / Ino80 complex / regulation of nucleotide-excision repair / adherens junction assembly / hepatocyte differentiation / Prefoldin mediated transfer of substrate to CCT/TriC / XY body / blastocyst formation / RSC-type complex / RHOF GTPase cycle / Adherens junctions interactions / RNA polymerase I preinitiation complex assembly / N-acetyltransferase activity / tight junction / positive regulation by host of viral transcription / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / regulation of mitotic metaphase/anaphase transition / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / ATP-dependent chromatin remodeler activity / SWI/SNF complex / positive regulation of double-strand break repair / regulation of synaptic vesicle endocytosis / germ cell nucleus / positive regulation of T cell differentiation / cardiac muscle cell proliferation / apical junction complex / cellular response to fatty acid / nuclear androgen receptor binding / establishment or maintenance of cell polarity / negative regulation of G1/S transition of mitotic cell cycle / regulation of cyclin-dependent protein serine/threonine kinase activity / nuclear chromosome / spinal cord development / regulation of chromosome organization / cortical cytoskeleton / maintenance of blood-brain barrier / homeostatic process / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of DNA replication / Recycling pathway of L1 / regulation of G1/S transition of mitotic cell cycle / kinesin binding / brush border / calyx of Held / negative regulation of cell differentiation / regulation of embryonic development / positive regulation of double-strand break repair via homologous recombination / positive regulation of Wnt signaling pathway / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / embryonic organ development / Chromatin modifying enzymes / regulation of DNA repair / DNA polymerase binding / heart morphogenesis / histone acetyltransferase activity / nucleosomal DNA binding / transcription initiation-coupled chromatin remodeling Similarity search - Function | ||||||
Biological species | ![]() ![]() unidentified (others) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
![]() | Chen, Z.C. / Chen, K.J. / Yuan, J.J. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 1023.9 KB | Display | ![]() |
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PDB format | ![]() | 767.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 128.3 KB | Display | |
Data in CIF | ![]() | 200.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 31926MC ![]() 7vdtC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Protein , 10 types, 15 molecules BFCGDHEKNPQRWXa
#1: Protein | Mass: 11394.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 14109.436 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 13965.265 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 15435.126 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #8: Protein | | Mass: 47509.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #9: Protein | | Mass: 41782.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #10: Protein | | Mass: 97547.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #11: Protein | | Mass: 58254.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #15: Protein | Mass: 133048.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #18: Protein | | Mass: 116762.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 63679.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#6: DNA chain | Mass: 64145.816 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Isoform 2 of ... , 2 types, 2 molecules AT
#7: Protein | Mass: 169597.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P51532, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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#12: Protein | Mass: 74385.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein/peptide , 2 types, 2 molecules UM
#13: Protein/peptide | Mass: 613.749 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: ![]() |
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#19: Protein/peptide | Mass: 1379.692 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: ![]() |
-SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily ... , 3 types, 3 molecules VYZ
#14: Protein | Mass: 44199.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#16: Protein | Mass: 60127.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#17: Protein | Mass: 46710.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 3 types, 3 molecules ![](data/chem/img/BEF.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
#20: Chemical | ChemComp-BEF / |
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#21: Chemical | ChemComp-MG / |
#22: 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 |
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Sample preparation
Component | Name: The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex Type: COMPLEX / Entity ID: #1-#19 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137659 / Symmetry type: POINT |