9RN2 | pdb_00009rn2

Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history. 

Literature

Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2

Vecchia, L., Weiss, J., Cavadini, S., Kempf, G., Kater, L., Pathare, G., Thoma, N.H.

To be published.

Macromolecule Content 

  • Total Structure Weight: 1,269.13 kDa 
  • Atom Count: 23,353 
  • Modeled Residue Count: 3,368 
  • Deposited Residue Count: 10,715 
  • Unique protein chains: 14
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3.1
A, E
139Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P68431 (Homo sapiens)
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PHAROS:  P68431
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UniProt GroupP68431
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H4
B, F
106Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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PHAROS:  P62805
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UniProt GroupP62805
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/E
C, G
133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens)
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PHAROS:  P04908
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UniProt GroupP04908
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2B type 1-J
D, H
128Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJ, H2BFR
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens)
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GTEx:  ENSG00000124635 
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UniProt GroupP06899
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcription activator BRG11,647Homo sapiensMutation(s): 0 
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P51532 (Homo sapiens)
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PHAROS:  P51532
GTEx:  ENSG00000127616 
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UniProt GroupP51532
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Actin-like protein 6A429Homo sapiensMutation(s): 0 
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Find proteins for O96019 (Homo sapiens)
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PHAROS:  O96019
GTEx:  ENSG00000136518 
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Actin, cytoplasmic 1, N-terminally processed375Homo sapiensMutation(s): 0 
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P60709 (Homo sapiens)
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PHAROS:  P60709
GTEx:  ENSG00000075624 
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
AT-rich interactive domain-containing protein 1A2,285Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O14497 (Homo sapiens)
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GTEx:  ENSG00000117713 
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1385Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q12824 (Homo sapiens)
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PHAROS:  Q12824
GTEx:  ENSG00000099956 
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
SWI/SNF complex subunit SMARCC2
N, O
1,214Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TAQ2 (Homo sapiens)
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PHAROS:  Q8TAQ2
GTEx:  ENSG00000139613 
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Reference Sequence
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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 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96GM5 (Homo sapiens)
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PHAROS:  Q96GM5
GTEx:  ENSG00000066117 
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Zinc finger protein ubi-d4Q [auth R]435Homo sapiensMutation(s): 0 
Gene Names: DPF2, BAF45D, REQ, UBID4
UniProt & NIH Common Fund Data Resources
Find proteins for Q92785 (Homo sapiens)
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PHAROS:  Q92785
GTEx:  ENSG00000133884 
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Green fluorescent protein,POU domain, class 5, transcription factor 1R [auth V]645Aequorea victoria, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Gene Names: GFP, POU5F1, OCT3, OCT4, OTF3
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Find proteins for P42212 (Aequorea victoria)
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Find proteins for Q01860 (Homo sapiens)
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PHAROS:  Q01860
GTEx:  ENSG00000204531 
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UniProt GroupsP42212Q01860
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcription factor SOX-2S [auth W]105Homo sapiensMutation(s): 0 
Gene Names: SOX2
UniProt & NIH Common Fund Data Resources
Find proteins for P48431 (Homo sapiens)
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PHAROS:  P48431
GTEx:  ENSG00000181449 
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UniProt GroupP48431
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Reference Sequence
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Entity ID: 15
MoleculeChains LengthOrganismImage
DNA (147-MER)T [auth X]227synthetic construct
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Entity ID: 16
MoleculeChains LengthOrganismImage
DNA (147-MER)U [auth Y]227synthetic construct
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--
Swiss National Science FoundationSwitzerland--
European Molecular Biology Organization (EMBO)European Union--
Other private--
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-11
    Type: Initial release