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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
TitleThe overall structure of human chromatin remodeling PBAF-nucleosome complex
Components
  • (DNA (207-MER)) x 2
  • (Isoform 2 of ...) x 2
  • (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily ...) x 3
  • (unknown) x 2
  • AT-rich interactive domain-containing protein 2,AT-rich interactive domain-containing protein 2
  • Actin, cytoplasmic 1
  • Actin-like protein 6A
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3
  • Histone H4
  • PHD finger protein 10
  • Protein polybromo-1
  • SWI/SNF complex subunit SMARCC2
KeywordsDNA BINDING PROTEIN / 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 norepinephrine uptake / bBAF complex / GBAF complex / brahma complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / cellular response to cytochalasin B ...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 norepinephrine uptake / bBAF complex / GBAF complex / brahma complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / cellular response to cytochalasin B / neural retina development / Formation of the embryonic stem cell BAF (esBAF) complex / npBAF complex / nBAF complex / negative regulation of androgen receptor signaling pathway / N-acetyltransferase activity / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Formation of the canonical BAF (cBAF) complex / regulation of transepithelial transport / coronary artery morphogenesis / morphogenesis of a polarized epithelium / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / Formation of the polybromo-BAF (pBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / structural constituent of postsynaptic actin cytoskeleton / Gap junction degradation / protein localization to adherens junction / Formation of the non-canonical BAF (ncBAF) complex / regulation of G0 to G1 transition / Cell-extracellular matrix interactions / dense body / RSC-type complex / Folding of actin by CCT/TriC / nucleosome array spacer activity / Tat protein binding / histone H3K14ac reader activity / RNA polymerase I preinitiation complex assembly / homeostatic process / Ino80 complex / postsynaptic actin cytoskeleton / XY body / cellular response to fatty acid / Regulation of CDH1 Function / regulation of double-strand break repair / host-mediated activation of viral transcription / apical protein localization / Prefoldin mediated transfer of substrate to CCT/TriC / Adherens junctions interactions / adherens junction assembly / RHOF GTPase cycle / regulation of nucleotide-excision repair / ATP-dependent chromatin remodeler activity / Sensory processing of sound by outer hair cells of the cochlea / SWI/SNF complex / nucleosome disassembly / tight junction / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / Interaction between L1 and Ankyrins / positive regulation of T cell differentiation / negative regulation of G1/S transition of mitotic cell cycle / nuclear androgen receptor binding / apical junction complex / histone acetyltransferase activity / maintenance of blood-brain barrier / positive regulation of stem cell population maintenance / nuclear chromosome / spinal cord development / regulation of chromosome organization / NuA4 histone acetyltransferase complex / regulation of norepinephrine uptake / transporter regulator activity / positive regulation of double-strand break repair / Recycling pathway of L1 / cortical cytoskeleton / Regulation of MITF-M-dependent genes involved in pigmentation / establishment or maintenance of cell polarity / regulation of DNA replication / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / nitric-oxide synthase binding / cardiac muscle cell proliferation / brush border / embryonic organ development / heart morphogenesis / EPH-ephrin mediated repulsion of cells / regulation of embryonic development / negative regulation of cell differentiation / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / RHO GTPases Activate WASPs and WAVEs / kinesin binding / positive regulation of Wnt signaling pathway / ATP-dependent activity, acting on DNA / histone reader activity / positive regulation of signal transduction by p53 class mediator / regulation of protein localization to plasma membrane / RHO GTPases activate IQGAPs / positive regulation of double-strand break repair via homologous recombination / Regulation of TP53 Activity through Acetylation
Similarity search - Function
PHD finger protein 10 / RFX DNA-binding domain / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / : / SWIB domain / SWI complex, BAF60b domains / SMARCC, SWIRM-associated domain / SMARCC, N-terminal / : / SWIRM-associated domain at the N-terminal ...PHD finger protein 10 / RFX DNA-binding domain / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / : / 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. / DNA-binding RFX-type winged-helix domain / : / SWI/SNF Subunit INI1, DNA binding domain / RFX-type winged-helix DNA-binding domain profile. / Protein polybromo-1, Bromodomain 5 / Chromatin-remodeling complex component Sfh1/SNF5 / SWI/SNF complex subunit BRG1 / SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / Remodelling complex subunit Rsc/polybromo / Protein of unknown function DUF3512 / Domain of unknown function (DUF3512) / : / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / 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 / 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 / HSA domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / Helicase/SANT-associated domain / HSA domain profile. / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / Bromo adjacent homology domain / SWIB/MDM2 domain superfamily / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / SANT domain profile. / HMG (high mobility group) box / SANT domain / Chromo/chromo shadow domain / Chromatin organization modifier domain / HMG boxes A and B DNA-binding domains profile. / 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 / PHD-finger / BRCT domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Zinc finger PHD-type signature. / Zinc finger C2H2 type domain signature. / Actin / Actin family / Actin / Zinc finger PHD-type profile. / Zinc finger C2H2-type / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Actin-like protein 6A / Histone H2B 1.1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 / Actin, cytoplasmic 1 ...ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Actin-like protein 6A / Histone H2B 1.1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 / Actin, cytoplasmic 1 / Histone H4 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / AT-rich interactive domain-containing protein 2 / Histone H2A / Protein polybromo-1 / SWI/SNF complex subunit SMARCC2 / PHD finger protein 10 / 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
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
unidentified (others)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsChen, Z.C. / Chen, K.J. / Yuan, J.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: 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
DepositionSep 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.0May 18, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 18, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 18, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.1Sep 17, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: DNA (207-MER)
J: DNA (207-MER)
A: Isoform 2 of Transcription activator BRG1
N: Actin-like protein 6A
P: Actin, cytoplasmic 1
Q: AT-rich interactive domain-containing protein 2,AT-rich interactive domain-containing protein 2
R: PHD finger protein 10
T: Isoform 2 of Bromodomain-containing protein 7
U: unknown
V: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
W: SWI/SNF complex subunit SMARCC2
X: SWI/SNF complex subunit SMARCC2
Y: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Z: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1
a: Protein polybromo-1
K: Histone H3
M: unknown
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,263,11827
Polymers1,262,60024
Non-polymers5183
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 10 types, 15 molecules BFCGDHEKNPQRWXa

#1: Protein Histone H4


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
#2: Protein Histone H2A


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
#3: Protein Histone H2B 1.1 / H2B1.1


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
#4: Protein Histone H3


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
#8: Protein Actin-like protein 6A / 53 kDa BRG1-associated factor A / Actin-related protein Baf53a / ArpNbeta / BRG1-associated factor ...53 kDa BRG1-associated factor A / Actin-related protein Baf53a / ArpNbeta / BRG1-associated factor 53A / BAF53A / INO80 complex subunit K


Mass: 47509.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARP4 / Production host: Homo sapiens (human) / References: UniProt: O96019
#9: Protein Actin, cytoplasmic 1 / Beta-actin


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: P60709
#10: Protein AT-rich interactive domain-containing protein 2,AT-rich interactive domain-containing protein 2 / ARID domain-containing protein 2 / BRG1-associated factor 200 / BAF200 / Zinc finger protein with ...ARID domain-containing protein 2 / BRG1-associated factor 200 / BAF200 / Zinc finger protein with activation potential / Zipzap/p200


Mass: 97547.102 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 PHD finger protein 10 / BRG1-associated factor 45a / BAF45a / XAP135


Mass: 58254.164 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
#15: Protein SWI/SNF complex subunit SMARCC2 / BRG1-associated factor 170 / BAF170


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
#18: Protein Protein polybromo-1 / hPB1 / BRG1-associated factor 180 / BAF180 / Polybromo-1D


Mass: 116762.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PBRM1, BAF180, PB1 / Production host: Homo sapiens (human) / References: UniProt: Q86U86

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (207-MER)


Mass: 63679.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (207-MER)


Mass: 64145.816 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Isoform 2 of ... , 2 types, 2 molecules AT

#7: Protein Isoform 2 of Transcription activator BRG1 / ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and ...ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and transcription activator / Protein BRG-1 / Protein brahma homolog 1 / SNF2-beta / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4


Mass: 169597.938 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, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#12: Protein Isoform 2 of Bromodomain-containing protein 7 / 75 kDa bromodomain protein / Protein CELTIX-1


Mass: 74385.812 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

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Protein/peptide , 2 types, 2 molecules UM

#13: Protein/peptide unknown


Mass: 613.749 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Homo sapiens (human)
#19: Protein/peptide unknown


Mass: 1379.692 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Homo sapiens (human)

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

#14: 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
#16: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / 60 kDa BRG-1/Brm-associated factor subunit A / BRG1-associated factor 60A / BAF60A / SWI/SNF ...60 kDa BRG-1/Brm-associated factor subunit A / BRG1-associated factor 60A / BAF60A / SWI/SNF complex 60 kDa subunit


Mass: 60127.332 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
#17: 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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Non-polymers , 3 types, 3 molecules

#20: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationN

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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: The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex
Type: COMPLEX / Entity ID: #1-#19 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137659 / Symmetry type: POINT

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