+Open data
-Basic information
Entry | Database: PDB / ID: 7y8r | |||||||||
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Title | The nucleosome-bound human PBAF complex | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / chromatin remodeling complexes / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / positive regulation of glucose mediated signaling pathway / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / blastocyst hatching / bBAF complex / npBAF complex / brahma complex / nBAF complex ...single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / positive regulation of glucose mediated signaling pathway / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / blastocyst hatching / bBAF complex / npBAF complex / brahma 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 / XY body / EGR2 and SOX10-mediated initiation of Schwann cell myelination / regulation of double-strand break repair / Ino80 complex / coronary artery morphogenesis / nucleosome disassembly / regulation of nucleotide-excision repair / RSC-type complex / hepatocyte differentiation / blastocyst formation / RNA polymerase I preinitiation complex assembly / N-acetyltransferase activity / 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 / germ cell nucleus / positive regulation of T cell differentiation / cardiac muscle cell proliferation / NuA4 histone acetyltransferase complex / cellular response to fatty acid / nuclear androgen receptor binding / regulation of chromosome organization / negative regulation of G1/S transition of mitotic cell cycle / nuclear chromosome / homeostatic process / spinal cord development / positive regulation of stem cell population maintenance / positive regulation of double-strand break repair via homologous recombination / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle / regulation of DNA replication / negative regulation of cell differentiation / regulation of embryonic development / positive regulation of Wnt signaling pathway / positive regulation of myoblast differentiation / embryonic organ development / ATP-dependent activity, acting on DNA / Chromatin modifying enzymes / regulation of DNA repair / DNA polymerase binding / Packaging Of Telomere Ends / heart morphogenesis / 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 / 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 / positive regulation of DNA repair / Meiotic synapsis / telomere maintenance / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / neurogenesis / Assembly of the ORC complex at the origin of replication / DNA methylation / negative regulation of cell migration / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / helicase activity / 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 / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Formation of the beta-catenin:TCF transactivating complex / DNA Damage Recognition in GG-NER / lysine-acetylated histone binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Wang, L. / Yu, J. / Yu, Z. / Wang, Q. / He, S. / Xu, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Commun / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y8r.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7y8r.ent.gz | 808.8 KB | Display | PDB format |
PDBx/mmJSON format | 7y8r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/7y8r ftp://data.pdbj.org/pub/pdb/validation_reports/y8/7y8r | HTTPS FTP |
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-Related structure data
Related structure data | 33684MC 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 , 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.) Homo sapiens (human) / Gene: LOC101372593 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A2U3ZMZ6 #2: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LOC102367360 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: H3A5H1 #3: Protein | Mass: 14004.329 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H2AC6, H2AFL, HIST1H2AC Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q93077 #4: Protein | Mass: 13806.018 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LOC102524608 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: S9WX78 #6: Protein | | Mass: 184923.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4 / Production host: Homo sapiens (human) / References: UniProt: P51532 #7: Protein | | Mass: 41782.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Actb / Production host: Homo sapiens (human) / References: UniProt: A0A7K5XZZ2 #8: Protein | | Mass: 47509.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACTL6A / Production host: Homo sapiens (human) / References: UniProt: O96019 #9: Protein | | Mass: 197581.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARID2 / Production host: Homo sapiens (human) / References: UniProt: Q68CP9 #11: Protein | Mass: 133048.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCC2 / Production host: Homo sapiens (human) / References: UniProt: Q8TAQ2 #15: Protein | | Mass: 56131.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PHF10 / Production host: Homo sapiens (human) / References: UniProt: Q8WUB8 #16: Protein | | Mass: 74257.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD7 / Production host: Homo sapiens (human) / References: UniProt: Q9NPI1 #18: Protein | | Mass: 184157.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PBRM1 / Production host: Homo sapiens (human) / References: UniProt: Q86U86 #19: Protein | | Mass: 8698.714 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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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.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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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.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#17: Protein/peptide | Mass: 1890.321 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#22: Protein/peptide | Mass: 2060.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-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.) Homo sapiens (human) / Gene: SMARCB1 / Production host: Homo sapiens (human) / References: UniProt: Q12824 |
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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.) Homo sapiens (human) / Gene: SMARCD1 / Production host: Homo sapiens (human) / References: UniProt: Q96GM5 |
#14: Protein | Mass: 46710.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCE1 / Production host: Homo sapiens (human) / References: UniProt: Q969G3 |
-DNA chain , 2 types, 2 molecules XY
#20: DNA chain | Mass: 65534.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#21: DNA chain | Mass: 65998.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Non-polymers , 3 types, 3 molecules
#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 |
-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: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
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 / 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) |
-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 |