8G86

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3
A, E
135Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P84233 (Xenopus laevis)
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Go to UniProtKB:  P84233
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UniProt GroupP84233
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
102Xenopus laevis laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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UniProt GroupP62799
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A
C, G
129Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajh2ac14LOC494591XELAEV_18003602mg
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis)
Explore Q6AZJ8 
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UniProt GroupQ6AZJ8
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B
D, H
122Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P02281 (Xenopus laevis)
Explore P02281 
Go to UniProtKB:  P02281
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UniProt GroupP02281
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Entity ID: 5
MoleculeChains LengthOrganismImage
nMatn1 DNA (top stand)186Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
nMatn1 DNA (bottom strand)186Homo sapiens
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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: 2023-05-24
    Changes: Database references
  • Version 1.2: 2023-06-07
    Changes: Database references
  • Version 1.3: 2023-07-26
    Changes: Database references
  • Version 1.4: 2024-06-19
    Changes: Data collection