8DK5

Structure of 187bp LIN28b nucleosome with site 0 mutation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1
A, E
136Homo 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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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
103Homo 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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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 2-C
C, G
129Homo sapiensMutation(s): 0 
Gene Names: H2AC20H2AFQHIST2H2AC
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Find proteins for Q16777 (Homo sapiens)
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GTEx:  ENSG00000184260 
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UniProt GroupQ16777
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 2-E
D, H
126Homo sapiensMutation(s): 0 
Gene Names: H2BC21H2BFQHIST2H2BE
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Find proteins for Q16778 (Homo sapiens)
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GTEx:  ENSG00000184678 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Single-chain variable fragmentI [auth K],
J [auth N]
265Mus musculusMutation(s): 0 
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (187-MER)K [auth I]187Homo sapiens
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (187-MER)L [auth J]187Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.71 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 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: 2024-11-13
    Changes: Data collection, Structure summary