8G87

Human Oct4 bound to nucleosome with human nMatn1 sequence (focused refinement of Oct4 bound region)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Histone modifications regulate pioneer transcription factor cooperativity.

Sinha, K.K.Bilokapic, S.Du, Y.Malik, D.Halic, M.

(2023) Nature 619: 378-384

  • DOI: https://doi.org/10.1038/s41586-023-06112-6
  • Primary Citation of Related Structures:  
    8G86, 8G87, 8G88, 8G8B, 8G8E, 8G8G

  • PubMed Abstract: 

    Pioneer transcription factors have the ability to access DNA in compacted chromatin 1 . Multiple transcription factors can bind together to a regulatory element in a cooperative way, and cooperation between the pioneer transcription factors OCT4 (also known as POU5F1) and SOX2 is important for pluripotency and reprogramming 2-4 . However, the molecular mechanisms by which pioneer transcription factors function and cooperate on chromatin remain unclear. Here we present cryo-electron microscopy structures of human OCT4 bound to a nucleosome containing human LIN28B or nMATN1 DNA sequences, both of which bear multiple binding sites for OCT4. Our structural and biochemistry data reveal that binding of OCT4 induces changes to the nucleosome structure, repositions the nucleosomal DNA and facilitates cooperative binding of additional OCT4 and of SOX2 to their internal binding sites. The flexible activation domain of OCT4 contacts the N-terminal tail of histone H4, altering its conformation and thus promoting chromatin decompaction. Moreover, the DNA-binding domain of OCT4 engages with the N-terminal tail of histone H3, and post-translational modifications at H3K27 modulate DNA positioning and affect transcription factor cooperativity. Thus, our findings suggest that the epigenetic landscape could regulate OCT4 activity to ensure proper cell programming.


  • Organizational Affiliation

    Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
POU domain, class 5, transcription factor 1C [auth X]395Homo sapiensMutation(s): 0 
Gene Names: POU5F1OCT3OCT4OTF3
UniProt & NIH Common Fund Data Resources
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 GroupQ01860
Sequence Annotations
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  • Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
nMatn1 DNA (top strand)A [auth I]186Homo sapiens
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
nMatn1 DNA (bottom strand)B [auth J]186Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM135599-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM141694-01

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release
  • Version 1.1: 2023-05-17
    Changes: Data processing
  • Version 1.2: 2023-05-24
    Changes: Database references
  • Version 1.3: 2023-06-07
    Changes: Database references
  • Version 1.4: 2023-07-26
    Changes: Database references
  • Version 1.5: 2024-06-19
    Changes: Data collection