9RN1 | pdb_00009rn1

Structure of BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in ADP-bound state, BAF47 bound to ATPase lobe 2

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.90 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 BAF-nucleosome complex with OCT4-SOX2 at SHL+6 in ADP-bound state, BAF47 bound to ATPase lobe 2

Na, N.A.

To be published.

Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1
A, E
139Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68431
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
106Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
PHAROS:  P62805
GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62805
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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)
Explore P04908 
Go to UniProtKB:  P04908
PHAROS:  P04908
GTEx:  ENSG00000277075 ENSG00000278463 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04908
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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)
Explore P06899 
Go to UniProtKB:  P06899
PHAROS:  P06899
GTEx:  ENSG00000124635 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06899
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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)
Explore P51532 
Go to UniProtKB:  P51532
PHAROS:  P51532
GTEx:  ENSG00000127616 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51532
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-like protein 6A429Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O96019 (Homo sapiens)
Explore O96019 
Go to UniProtKB:  O96019
PHAROS:  O96019
GTEx:  ENSG00000136518 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO96019
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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)
Explore P60709 
Go to UniProtKB:  P60709
PHAROS:  P60709
GTEx:  ENSG00000075624 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60709
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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)
Explore O14497 
Go to UniProtKB:  O14497
PHAROS:  O14497
GTEx:  ENSG00000117713 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14497
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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)
Explore Q12824 
Go to UniProtKB:  Q12824
PHAROS:  Q12824
GTEx:  ENSG00000099956 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12824
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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)
Explore Q8TAQ2 
Go to UniProtKB:  Q8TAQ2
PHAROS:  Q8TAQ2
GTEx:  ENSG00000139613 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TAQ2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
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)
Explore Q96GM5 
Go to UniProtKB:  Q96GM5
PHAROS:  Q96GM5
GTEx:  ENSG00000066117 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96GM5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1411Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q969G3 (Homo sapiens)
Explore Q969G3 
Go to UniProtKB:  Q969G3
PHAROS:  Q969G3
GTEx:  ENSG00000073584 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ969G3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger protein ubi-d4435Homo sapiensMutation(s): 0 
Gene Names: DPF2, BAF45D, REQ, UBID4
UniProt & NIH Common Fund Data Resources
Find proteins for Q92785 (Homo sapiens)
Explore Q92785 
Go to UniProtKB:  Q92785
PHAROS:  Q92785
GTEx:  ENSG00000133884 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92785
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Green fluorescent protein,POU domain, class 5, transcription factor 1S [auth V]645Aequorea victoria, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Gene Names: GFP, POU5F1, OCT3, OCT4, OTF3
UniProt & NIH Common Fund Data Resources
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Find proteins for Q01860 (Homo sapiens)
Explore Q01860 
Go to UniProtKB:  Q01860
PHAROS:  Q01860
GTEx:  ENSG00000204531 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP42212Q01860
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor SOX-2T [auth W]105Homo sapiensMutation(s): 0 
Gene Names: SOX2
UniProt & NIH Common Fund Data Resources
Find proteins for P48431 (Homo sapiens)
Explore P48431 
Go to UniProtKB:  P48431
PHAROS:  P48431
GTEx:  ENSG00000181449 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48431
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains LengthOrganismImage
DNA (148-MER)U [auth X]227synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains LengthOrganismImage
DNA (148-MER)V [auth Y]227synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland--
European Research Council (ERC)European Union--
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