6LTH

Structure of human BAF Base module


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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
Transcription activator BRG1A [auth I]1,647Homo sapiensMutation(s): 0 
Gene Names: SMARCA4
EC: 3.6.4
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PHAROS:  P51532
GTEx:  ENSG00000127616 
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UniProt GroupP51532
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AT-rich interactive domain-containing protein 1AB [auth L]2,285Homo sapiensMutation(s): 0 
Gene Names: ARID1A
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PHAROS:  O14497
GTEx:  ENSG00000117713 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1C [auth M]385Homo sapiensMutation(s): 0 
Gene Names: SMARCB1
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PHAROS:  Q12824
GTEx:  ENSG00000099956 
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UniProt GroupQ12824
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
SWI/SNF complex subunit SMARCC2D [auth N],
E [auth O]
1,214Homo sapiensMutation(s): 0 
Gene Names: SMARCC2
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GTEx:  ENSG00000139613 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1F [auth P]515Homo sapiensMutation(s): 0 
Gene Names: SMARCD1
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GTEx:  ENSG00000066117 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1G [auth Q]411Homo sapiensMutation(s): 0 
Gene Names: SMARCE1
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PHAROS:  Q969G3
GTEx:  ENSG00000073584 
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UniProt GroupQ969G3
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger protein ubi-d4H [auth R]391Homo sapiensMutation(s): 0 
Gene Names: DPF2
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GTEx:  ENSG00000133884 
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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 
I [auth L]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.12.4
MODEL REFINEMENTPHENIX1.16

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