7VDV

The overall structure of human chromatin remodeling PBAF-nucleosome complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure of human chromatin-remodelling PBAF complex bound to a nucleosome.

Yuan, J.J.Chen, K.J.Zhang, W.B.Chen, Z.C.

(2022) Nature 605: 166-171

  • DOI: https://doi.org/10.1038/s41586-022-04658-5
  • Primary Citation of Related Structures:  
    7VDT, 7VDV

  • PubMed Abstract: 

    DNA wraps around the histone octamer to form nucleosomes 1 , 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 2,3 . 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.


  • Organizational Affiliation

    MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4A [auth B],
E [auth F]
103Xenopus laevisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2AB [auth C],
F [auth G]
130Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591XELAEV_18003602mg
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1C [auth D],
G [auth H]
126Xenopus laevisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3D [auth E],
W [auth K]
136Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18002543mg
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Transcription activator BRG1J [auth A]1,485Homo sapiensMutation(s): 0 
Gene Names: SMARCA4
EC: 3.6.4
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GTEx:  ENSG00000127616 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-like protein 6AK [auth N]429Homo sapiensMutation(s): 0 
Gene Names: ARP4
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GTEx:  ENSG00000136518 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, cytoplasmic 1L [auth P]375Homo sapiensMutation(s): 0 
Gene Names: ACTB
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GTEx:  ENSG00000075624 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
AT-rich interactive domain-containing protein 2,AT-rich interactive domain-containing protein 2M [auth Q]870Homo sapiensMutation(s): 0 
Gene Names: ARID2
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GTEx:  ENSG00000189079 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
PHD finger protein 10N [auth R]514Homo sapiensMutation(s): 0 
Gene Names: PHF10
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GTEx:  ENSG00000130024 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Bromodomain-containing protein 7O [auth T]652Homo sapiensMutation(s): 0 
Gene Names: BRD7
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GTEx:  ENSG00000166164 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
unknownP [auth U]7unidentifiedMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1Q [auth V]385Homo sapiensMutation(s): 0 
Gene Names: SMARCB1
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GTEx:  ENSG00000099956 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
SWI/SNF complex subunit SMARCC2R [auth W],
S [auth X]
1,214Homo sapiensMutation(s): 0 
Gene Names: SMARCC2
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GTEx:  ENSG00000139613 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1T [auth Y]529Homo sapiensMutation(s): 0 
Gene Names: SMARCD1
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GTEx:  ENSG00000066117 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1U [auth Z]411Homo sapiensMutation(s): 0 
Gene Names: SMARCE1
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GTEx:  ENSG00000073584 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Protein polybromo-1V [auth a]1,020Homo sapiensMutation(s): 0 
Gene Names: PBRM1BAF180PB1
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GTEx:  ENSG00000163939 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
unknownX [auth M]16unidentifiedMutation(s): 0 
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (207-MER)H [auth I]207synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (207-MER)I [auth J]207synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release