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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 pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / positive regulation of glucose mediated signaling pathway / positive regulation of norepinephrine uptake / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / cellular response to cytochalasin B / bBAF complex / blastocyst hatching / npBAF 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 / positive regulation of norepinephrine uptake / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / cellular response to cytochalasin B / bBAF complex / blastocyst hatching / npBAF complex / postsynaptic actin cytoskeleton organization / regulation of transepithelial transport / brahma complex / nBAF complex / structural constituent of postsynaptic actin cytoskeleton / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of androgen receptor signaling pathway / morphogenesis of a polarized epithelium / Formation of annular gap junctions / neural retina development / GBAF complex / Gap junction degradation / postsynaptic actin cytoskeleton / protein localization to adherens junction / regulation of G0 to G1 transition / dense body / Cell-extracellular matrix interactions / Tat protein binding / XY body / nucleosome disassembly / Folding of actin by CCT/TriC / regulation of double-strand break repair / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Ino80 complex / coronary artery morphogenesis / regulation of nucleotide-excision repair / RSC-type complex / apical protein localization / hepatocyte differentiation / blastocyst formation / Prefoldin mediated transfer of substrate to CCT/TriC / adherens junction assembly / RHOF GTPase cycle / Adherens junctions interactions / RNA polymerase I preinitiation complex assembly / N-acetyltransferase activity / positive regulation by host of viral transcription / tight junction / Sensory processing of sound by outer hair cells of the cochlea / SWI/SNF complex / ATP-dependent chromatin remodeler activity / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / regulation of norepinephrine uptake / positive regulation of double-strand break repair / germ cell nucleus / positive regulation of T cell differentiation / NuA4 histone acetyltransferase complex / cardiac muscle cell proliferation / regulation of synaptic vesicle endocytosis / cellular response to fatty acid / apical junction complex / nuclear androgen receptor binding / regulation of chromosome organization / maintenance of blood-brain barrier / establishment or maintenance of cell polarity / negative regulation of G1/S transition of mitotic cell cycle / nuclear chromosome / homeostatic process / spinal cord development / cortical cytoskeleton / positive regulation of double-strand break repair via homologous recombination / positive regulation of stem cell population maintenance / nitric-oxide synthase binding / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Recycling pathway of L1 / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of G1/S transition of mitotic cell cycle / regulation of DNA replication / negative regulation of cell differentiation / brush border / regulation of embryonic development / kinesin binding / calyx of Held / positive regulation of Wnt signaling pathway / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / positive regulation of myoblast differentiation / embryonic organ development / regulation of DNA repair / ATP-dependent activity, acting on DNA / Chromatin modifying enzymes / regulation of protein localization to plasma membrane / DNA polymerase binding / heart morphogenesis / transcription initiation-coupled chromatin remodeling / positive regulation of DNA repair / Regulation of TP53 Activity through Acetylation
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 / MarR-like, BRCT and chromo domains module profile. ...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 / DNA-binding RFX-type winged-helix domain / SWI/SNF complex subunit BRG1 / 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) / domain in helicases and associated with SANT domains / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / SWIRM domain / SWIRM domain / SWIRM domain profile. / 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 / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SANT domain profile. / SWIB/MDM2 domain superfamily / SANT domain / : / Chromo/chromo shadow domain / Chromatin organization modifier domain / HMG (high mobility group) box / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / HMG boxes A and B DNA-binding domains profile. / Myb-like DNA-binding domain / high mobility group / High mobility group box domain / High mobility group box domain superfamily / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / BRCT domain superfamily / PHD-finger / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. / Zinc finger C2H2-type / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold
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 / Transcription activator BRG1 / Actin, cytoplasmic 1 ...ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Actin-like protein 6A / Histone H2B 1.1 / Transcription activator BRG1 / 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

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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
Water0
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 / Adenosine 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

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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 FIELDBright-field microscopy
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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