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Open data
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Basic information
Entry | Database: PDB / ID: 7y8r | |||||||||
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Title | The nucleosome-bound human PBAF complex | |||||||||
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![]() | DNA BINDING PROTEIN/DNA / chromatin remodeling complexes / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA 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 / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / blastocyst hatching / bBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of androgen receptor signaling pathway / npBAF complex ...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 / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / blastocyst hatching / bBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of androgen receptor signaling pathway / npBAF complex / Tat protein binding / brahma complex / nBAF complex / GBAF complex / neural retina development / regulation of G0 to G1 transition / EGR2 and SOX10-mediated initiation of Schwann cell myelination / regulation of double-strand break repair / coronary artery morphogenesis / nucleosome disassembly / Ino80 complex / regulation of nucleotide-excision repair / hepatocyte differentiation / XY body / blastocyst formation / RSC-type complex / RNA polymerase I preinitiation complex assembly / N-acetyltransferase activity / positive regulation by host of viral transcription / regulation of mitotic metaphase/anaphase transition / ATP-dependent chromatin remodeler activity / SWI/SNF complex / positive regulation of double-strand break repair / germ cell nucleus / positive regulation of T cell differentiation / cardiac muscle cell proliferation / cellular response to fatty acid / nuclear androgen receptor binding / negative regulation of G1/S transition of mitotic cell cycle / nuclear chromosome / spinal cord development / regulation of chromosome organization / homeostatic process / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of DNA replication / regulation of G1/S transition of mitotic cell cycle / 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 / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / embryonic organ development / Chromatin modifying enzymes / regulation of DNA repair / DNA polymerase binding / heterochromatin organization / Packaging Of Telomere Ends / heart morphogenesis / histone acetyltransferase activity / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / transcription initiation-coupled chromatin remodeling / Regulation of TP53 Activity through Acetylation / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / regulation of mitotic cell cycle / Inhibition of DNA recombination at telomere / Meiotic synapsis / positive regulation of DNA repair / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / telomere maintenance / Assembly of the ORC complex at the origin of replication / negative regulation of cell migration / helicase activity / DNA methylation / neurogenesis / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / transcription coregulator binding / HDACs deacetylate histones / transcription elongation by RNA polymerase II / nuclear receptor binding / positive regulation of cell differentiation / RNA Polymerase I Promoter Escape / transcription coregulator activity / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA Damage Recognition in GG-NER Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
![]() | Wang, L. / Yu, J. / Yu, Z. / Wang, Q. / He, S. / Xu, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of nucleosome-bound human PBAF complex. Authors: Li Wang / Jiali Yu / Zishuo Yu / Qianmin Wang / Wanjun Li / Yulei Ren / Zhenguo Chen / Shuang He / Yanhui Xu / ![]() Abstract: BAF and PBAF are mammalian SWI/SNF family chromatin remodeling complexes that possess multiple histone/DNA-binding subunits and create nucleosome-depleted/free regions for transcription activation. ...BAF and PBAF are mammalian SWI/SNF family chromatin remodeling complexes that possess multiple histone/DNA-binding subunits and create nucleosome-depleted/free regions for transcription activation. Despite previous structural studies and recent advance of SWI/SNF family complexes, it remains incompletely understood how PBAF-nucleosome complex is organized. Here we determined structure of 13-subunit human PBAF in complex with acetylated nucleosome in ADP-BeF-bound state. Four PBAF-specific subunits work together with nine BAF/PBAF-shared subunits to generate PBAF-specific modular organization, distinct from that of BAF at various regions. PBAF-nucleosome structure reveals six histone-binding domains and four DNA-binding domains/modules, the majority of which directly bind histone/DNA. This multivalent nucleosome-binding pattern, not observed in previous studies, suggests that PBAF may integrate comprehensive chromatin information to target genomic loci for function. Our study reveals molecular organization of subunits and histone/DNA-binding domains/modules in PBAF-nucleosome complex and provides structural insights into PBAF-mediated nucleosome association complimentary to the recently reported PBAF-nucleosome structure. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 808.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 122.2 KB | Display | |
Data in CIF | ![]() | 191.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 33684MC 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 , 13 types, 18 molecules AEBFCGDHIJKLNORSUV
#1: Protein | Mass: 15305.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: A0A2U3ZMZ6 #2: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: H3A5H1 #3: Protein | Mass: 14004.329 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: Q93077 #4: Protein | Mass: 13806.018 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: S9WX78 #6: Protein | | Mass: 184923.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #7: Protein | | Mass: 41782.660 Da / Num. of mol.: 1 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: 197581.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #11: Protein | Mass: 133048.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #15: Protein | | Mass: 56131.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #16: Protein | | Mass: 74257.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #18: Protein | | Mass: 184157.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #19: Protein | | Mass: 8698.714 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Protein/peptide , 4 types, 4 molecules ZaTW
#5: Protein/peptide | Mass: 2486.056 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#12: Protein/peptide | Mass: 1039.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#17: Protein/peptide | Mass: 1890.321 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#22: Protein/peptide | Mass: 2060.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily ... , 3 types, 3 molecules MPQ
#10: Protein | Mass: 44199.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#13: Protein | Mass: 58311.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#14: Protein | Mass: 46710.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-DNA chain , 2 types, 2 molecules XY
#20: DNA chain | Mass: 65534.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#21: DNA chain | Mass: 65998.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 3 types, 3 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/BEF.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/BEF.gif)
#23: Chemical | ChemComp-ADP / |
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#24: Chemical | ChemComp-MG / |
#25: Chemical | ChemComp-BEF / |
-Details
Has ligand of interest | N |
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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: Nucleosome-bound human PBAF complex / Type: COMPLEX / Entity ID: #1-#4, #7-#10, #13-#22 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 8 |
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 / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37528 / Symmetry type: POINT |