6LTJ

Structure of nucleosome-bound human BAF complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of nucleosome-bound human BAF complex.

He, S.Wu, Z.Tian, Y.Yu, Z.Yu, J.Wang, X.Li, J.Liu, B.Xu, Y.

(2020) Science 367: 875-881

  • DOI: https://doi.org/10.1126/science.aaz9761
  • Primary Citation of Related Structures:  
    6LTH, 6LTJ

  • PubMed Abstract: 

    Mammalian SWI/SNF family chromatin remodelers, BRG1/BRM-associated factor (BAF) and polybromo-associated BAF (PBAF), regulate chromatin structure and transcription, and their mutations are linked to cancers. The 3.7-angstrom-resolution cryo-electron microscopy structure of human BAF bound to the nucleosome reveals that the nucleosome is sandwiched by the base and the adenosine triphosphatase (ATPase) modules, which are bridged by the actin-related protein (ARP) module. The ATPase motor is positioned proximal to nucleosomal DNA and, upon ATP hydrolysis, engages with and pumps DNA along the nucleosome. The C-terminal α helix of SMARCB1, enriched in positively charged residues frequently mutated in cancers, mediates interactions with an acidic patch of the nucleosome. AT-rich interactive domain-containing protein 1A (ARID1A) and the SWI/SNF complex subunit SMARCC serve as a structural core and scaffold in the base module organization, respectively. Our study provides structural insights into subunit organization and nucleosome recognition of human BAF complex.


  • Organizational Affiliation

    Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.3
A, E
136Xenopus laevisMutation(s): 0 
UniProt
Find proteins for Q6PI79 (Xenopus laevis)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
103Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1
C, G
130Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B
D, H
126Xenopus laevisMutation(s): 0 
Gene Names: H2B
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription activator BRG11,647Homo sapiensMutation(s): 0 
Gene Names: SMARCA4
EC: 3.6.4
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PHAROS:  P51532
GTEx:  ENSG00000127616 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-like protein 6A407Homo sapiensMutation(s): 0 
Gene Names: ACTL6ABAF53BAF53A
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GTEx:  ENSG00000136518 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, cytoplasmic 1375Homo sapiensMutation(s): 0 
Gene Names: ACTB
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PHAROS:  P60709
GTEx:  ENSG00000075624 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
AT-rich interactive domain-containing protein 1A1,295Homo sapiensMutation(s): 0 
Gene Names: ARID1ABAF250BAF250A
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PHAROS:  O14497
GTEx:  ENSG00000117713 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1336Homo sapiensMutation(s): 0 
Gene Names: SMARCB1BAF47
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GTEx:  ENSG00000099956 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
SWI/SNF complex subunit SMARCC2
N, O
1,214Homo sapiensMutation(s): 0 
Gene Names: SMARCC2
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PHAROS:  Q8TAQ2
GTEx:  ENSG00000139613 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1515Homo sapiensMutation(s): 0 
Gene Names: SMARCD1
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GTEx:  ENSG00000066117 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1411Homo sapiensMutation(s): 0 
Gene Names: SMARCE1
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GTEx:  ENSG00000073584 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger protein ubi-d4292Homo sapiensMutation(s): 0 
Gene Names: DPF2BAF45D
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GTEx:  ENSG00000133884 
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Entity ID: 14
MoleculeChains LengthOrganismImage
DNA (119-MER)S [auth X]119Homo sapiens
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Entity ID: 15
MoleculeChains LengthOrganismImage
DNA (119-MER)T [auth Y]119Homo sapiens
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
U [auth L]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.8

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2021-08-25
    Changes: Database references, Structure summary
  • Version 1.2: 2021-10-13
    Changes: Database references