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- PDB-7vdv: The overall structure of human chromatin remodeling PBAF-nucleoso... -

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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 / histone H3K14ac reader activity / 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 / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of androgen receptor signaling pathway / bBAF complex ...single stranded viral RNA replication via double stranded DNA intermediate / histone H3K14ac reader activity / 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 / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of androgen receptor signaling pathway / bBAF complex / npBAF complex / regulation of transepithelial transport / nBAF complex / brahma complex / morphogenesis of a polarized epithelium / blastocyst hatching / neural retina development / protein localization to adherens junction / postsynaptic actin cytoskeleton / structural constituent of postsynaptic actin cytoskeleton / N-acetyltransferase activity / Formation of the dystrophin-glycoprotein complex (DGC) / GBAF complex / Formation of annular gap junctions / EGR2 and SOX10-mediated initiation of Schwann cell myelination / coronary artery morphogenesis / Tat protein binding / nucleosome array spacer activity / Gap junction degradation / regulation of G0 to G1 transition / Folding of actin by CCT/TriC / Cell-extracellular matrix interactions / dense body / hepatocyte differentiation / XY body / Ino80 complex / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / ATP-dependent chromatin remodeler activity / RSC-type complex / apical protein localization / regulation of double-strand break repair / blastocyst formation / RNA polymerase I preinitiation complex assembly / adherens junction assembly / RHOF GTPase cycle / Adherens junctions interactions / positive regulation by host of viral transcription / tight junction / nucleosome disassembly / Sensory processing of sound by outer hair cells of the cochlea / germ cell nucleus / Interaction between L1 and Ankyrins / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of T cell differentiation / cardiac muscle cell proliferation / cellular response to fatty acid / regulation of norepinephrine uptake / transporter regulator activity / apical junction complex / nuclear androgen receptor binding / nitric-oxide synthase binding / positive regulation of double-strand break repair / nuclear chromosome / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / homeostatic process / maintenance of blood-brain barrier / regulation of chromosome organization / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / cortical cytoskeleton / histone acetyltransferase activity / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / Recycling pathway of L1 / regulation of synaptic vesicle endocytosis / regulation of G1/S transition of mitotic cell cycle / regulation of DNA replication / brush border / regulation of embryonic development / kinesin binding / EPH-ephrin mediated repulsion of cells / negative regulation of cell differentiation / positive regulation of Wnt signaling pathway / ATP-dependent activity, acting on DNA / RHO GTPases Activate WASPs and WAVEs / embryonic organ development / positive regulation of myoblast differentiation / RHO GTPases activate IQGAPs / positive regulation of double-strand break repair via homologous recombination / regulation of DNA repair / regulation of protein localization to plasma membrane / heart morphogenesis / Chromatin modifying enzymes / Regulation of TP53 Activity through Acetylation / DNA polymerase binding
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 / : / 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) / 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. / HMG boxes A and B DNA-binding domains profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / 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. / : / Histone H2B signature. / Histone H2B / Histone H2B / Zinc finger C2H2-type / Zinc finger PHD-type profile. / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A
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
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

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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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