8SPU

Structure of ESRRB nucleosome bound OCT4 at site c


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Literature

Structural mechanism of LIN28B nucleosome targeting by OCT4.

Guan, R.Lian, T.Zhou, B.R.Wheeler, D.Bai, Y.

(2023) Mol Cell 83: 1970-1982.e6

  • DOI: https://doi.org/10.1016/j.molcel.2023.05.030
  • Primary Citation of Related Structures:  
    7U0G, 7U0I, 7U0J, 8DK5, 8SPS, 8SPU

  • PubMed Abstract: 

    Pioneer transcription factors are essential for cell fate changes by targeting closed chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However, the structural basis of how pioneer factors recognize the in vivo nucleosomal DNA targets is unknown. Here, we determine the high-resolution structures of the nucleosome containing human LIN28B DNA and its complexes with the OCT4 DNA binding region. Three OCT4s bind the pre-positioned nucleosome by recognizing non-canonical DNA sequences. Two use their POUS domains while the other uses the POUS-loop-POUHD region; POUHD serves as a wedge to unwrap ∼25 base pair DNA. Our analysis of previous genomic data and determination of the ESRRB-nucleosome-OCT4 structure confirmed the generality of these structural features. Moreover, biochemical studies suggest that multiple OCT4s cooperatively open the H1-condensed nucleosome array containing the LIN28B nucleosome. Thus, our study suggests a mechanism of how OCT4 can target the nucleosome and open closed chromatin.


  • Organizational Affiliation

    Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Maltodextrin-binding protein,POU domain, class 5, transcription factor 1C [auth L]550Homo sapiensMutation(s): 0 
Gene Names: malENCTC8450_00456NCTC9775_03059POU5F1OCT3OCT4OTF3
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PHAROS:  Q01860
GTEx:  ENSG00000204531 
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UniProt GroupQ01860
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1D [auth E],
H [auth A]
136Homo sapiensMutation(s): 0 
Gene Names: 
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PHAROS:  P68431
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UniProt GroupP68431
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4E [auth F],
I [auth B]
103Homo sapiensMutation(s): 0 
Gene Names: 
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UniProt GroupP62805
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 2-CF [auth G],
J [auth C]
129Homo sapiensMutation(s): 0 
Gene Names: H2AC20H2AFQHIST2H2AC
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GTEx:  ENSG00000184260 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 2-EG [auth H],
K [auth D]
126Homo sapiensMutation(s): 0 
Gene Names: H2BC21H2BFQHIST2H2BE
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GTEx:  ENSG00000184678 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ScFvL [auth N],
M [auth K]
265Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (168-MER)A [auth J]168Homo sapiens
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (168-MER)B [auth I]168Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20rc2_4400:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection
  • Version 1.2: 2024-10-16
    Changes: Data collection, Structure summary