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- PDB-7y8r: The nucleosome-bound human PBAF complex -

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Basic information

Entry
Database: PDB / ID: 7y8r
TitleThe nucleosome-bound human PBAF complex
Components
  • (DNA (213-MER)) x 2
  • (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily ...) x 3
  • (Unknown) x 4
  • ACTB protein (Fragment)
  • AT-rich interactive domain-containing protein 2
  • Actin-like protein 6A
  • Bromodomain-containing protein 7
  • Histone H2A type 1-C
  • Histone H2B
  • Histone H3
  • Histone H4
  • PHD finger protein 10
  • Protein polybromo-1
  • SWI/SNF complex subunit SMARCC2
  • Transcription activator BRG1
  • Unkown
KeywordsDNA 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 glucose mediated signaling pathway / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / bBAF complex / npBAF complex / nBAF complex / brahma complex / neural retina development ...single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / bBAF complex / npBAF complex / nBAF complex / brahma complex / neural retina development / negative regulation of androgen receptor signaling pathway / N-acetyltransferase activity / histone H3K14ac reader activity / GBAF complex / blastocyst hatching / EGR2 and SOX10-mediated initiation of Schwann cell myelination / nucleosome array spacer activity / regulation of G0 to G1 transition / hepatocyte differentiation / Tat protein binding / coronary artery morphogenesis / XY body / Ino80 complex / RSC-type complex / regulation of double-strand break repair / blastocyst formation / regulation of nucleotide-excision repair / RNA polymerase I preinitiation complex assembly / ATP-dependent chromatin remodeler activity / cellular response to fatty acid / host-mediated activation of viral transcription / nucleosome disassembly / germ cell nucleus / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / nuclear androgen receptor binding / positive regulation of double-strand break repair / nuclear chromosome / negative regulation of G1/S transition of mitotic cell cycle / homeostatic process / spinal cord development / regulation of chromosome organization / NuA4 histone acetyltransferase complex / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of DNA replication / regulation of G1/S transition of mitotic cell cycle / regulation of embryonic development / negative regulation of cell differentiation / positive regulation of signal transduction by p53 class mediator / positive regulation of Wnt signaling pathway / cardiac muscle cell proliferation / ATP-dependent activity, acting on DNA / positive regulation of myoblast differentiation / embryonic organ development / heart morphogenesis / positive regulation of double-strand break repair via homologous recombination / histone acetyltransferase activity / regulation of DNA repair / Chromatin modifying enzymes / Packaging Of Telomere Ends / Regulation of TP53 Activity through Acetylation / : / DNA polymerase binding / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / neurogenesis / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Interleukin-7 signaling / telomere maintenance / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / transcription initiation-coupled chromatin remodeling / Assembly of the ORC complex at the origin of replication / regulation of mitotic cell cycle / positive regulation of DNA repair / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / negative regulation of cell migration / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / nuclear receptor binding / transcription coregulator binding / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / DNA Damage Recognition in GG-NER / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / positive regulation of cell differentiation / transcription coregulator activity / HDACs deacetylate histones / RNA Polymerase I Promoter Escape
Similarity search - Function
PHD finger protein 10 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / RFX DNA-binding domain / SWIB domain / SWI complex, BAF60b domains / SMARCC, SWIRM-associated domain / SMARCC, N-terminal / : / SWIRM-associated domain at the N-terminal / SWIRM-associated domain at the C-terminal ...PHD finger protein 10 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / RFX DNA-binding domain / SWIB domain / SWI complex, BAF60b domains / SMARCC, SWIRM-associated domain / SMARCC, N-terminal / : / SWIRM-associated domain at the N-terminal / SWIRM-associated domain at the C-terminal / MarR-like, BRCT and chromo domains module profile. / : / SWI/SNF Subunit INI1, DNA binding domain / : / SWI/SNF complex subunit BRG1 / DNA-binding RFX-type winged-helix domain / RFX-type winged-helix DNA-binding domain profile. / Chromatin-remodeling complex component Sfh1/SNF5 / Protein polybromo-1, Bromodomain 5 / SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Remodelling complex subunit Rsc/polybromo / Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / : / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / domain in helicases and associated with SANT domains / HSA domain / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / ARID/BRIGHT DNA binding domain / Helicase/SANT-associated domain / HSA domain profile. / SWIRM domain / SWIRM domain / SWIRM domain profile. / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / SWIB/MDM2 domain superfamily / HMG (high mobility group) box / SANT domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / HMG boxes A and B DNA-binding domains profile. / SANT domain / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Myb-like DNA-binding domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / BRCT domain superfamily / PHD-finger / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Zinc finger PHD-type signature. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Zinc finger PHD-type profile. / : / Zinc finger, PHD-finger / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H3 / ACTB protein / Histone H4 / Actin-like protein 6A / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 ...ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H3 / ACTB protein / Histone H4 / Actin-like protein 6A / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / AT-rich interactive domain-containing protein 2 / Protein polybromo-1 / SWI/SNF complex subunit SMARCC2 / PHD finger protein 10 / Histone H2A type 1-C / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / Bromodomain-containing protein 7 / Histone H2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsWang, L. / Yu, J. / Yu, Z. / Wang, Q. / He, S. / Xu, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32030055 China
National Natural Science Foundation of China (NSFC) China
CitationJournal: 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
DepositionJun 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3
B: Histone H4
C: Histone H2A type 1-C
D: Histone H2B
E: Histone H3
F: Histone H4
G: Histone H2A type 1-C
H: Histone H2B
Z: Unknown
I: Transcription activator BRG1
J: ACTB protein (Fragment)
K: Actin-like protein 6A
L: AT-rich interactive domain-containing protein 2
M: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
N: SWI/SNF complex subunit SMARCC2
a: Unknown
O: SWI/SNF complex subunit SMARCC2
P: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Q: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1
R: PHD finger protein 10
S: Bromodomain-containing protein 7
T: Unkown
U: Protein polybromo-1
V: Unknown
X: DNA (213-MER)
Y: DNA (213-MER)
W: Unknown
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,458,64630
Polymers1,458,12827
Non-polymers5183
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 13 types, 18 molecules AEBFCGDHIJKLNORSUV

#1: Protein Histone H3


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 Histone H4


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 Histone H2A type 1-C / H2A-clustered histone 6 / Histone H2A/l


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 Histone H2B


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 Transcription activator BRG1


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 ACTB protein (Fragment)


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 Actin-like protein 6A


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 AT-rich interactive domain-containing protein 2


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 SWI/SNF complex subunit SMARCC2


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 PHD finger protein 10


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 Bromodomain-containing protein 7


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 Protein polybromo-1


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 Unknown


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 Unknown


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)
#12: Protein/peptide Unknown


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 Unkown


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 Unknown


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)

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SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily ... , 3 types, 3 molecules MPQ

#10: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1


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
#13: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1


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 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1


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

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DNA chain , 2 types, 2 molecules XY

#20: DNA chain DNA (213-MER)


Mass: 65534.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#21: DNA chain DNA (213-MER)


Mass: 65998.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 3 molecules

#23: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#24: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#25: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Nucleosome-bound human PBAF complex / Type: COMPLEX / Entity ID: #1-#4, #7-#10, #13-#22 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37528 / Symmetry type: POINT

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