6T79

Structure of a human nucleosome at 3.2 A resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


Literature

Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function.

Dodonova, S.O.Zhu, F.Dienemann, C.Taipale, J.Cramer, P.

(2020) Nature 580: 669-672

  • DOI: https://doi.org/10.1038/s41586-020-2195-y
  • Primary Citation of Related Structures:  
    6T78, 6T79, 6T7A, 6T7B, 6T7C, 6T7D

  • PubMed Abstract: 

    'Pioneer' transcription factors are required for stem-cell pluripotency, cell differentiation and cell reprogramming 1,2 . Pioneer factors can bind nucleosomal DNA to enable gene expression from regions of the genome with closed chromatin. SOX2 is a prominent pioneer factor that is essential for pluripotency and self-renewal of embryonic stem cells 3 . Here we report cryo-electron microscopy structures of the DNA-binding domains of SOX2 and its close homologue SOX11 bound to nucleosomes. The structures show that SOX factors can bind and locally distort DNA at superhelical location 2. The factors also facilitate detachment of terminal nucleosomal DNA from the histone octamer, which increases DNA accessibility. SOX-factor binding to the nucleosome can also lead to a repositioning of the N-terminal tail of histone H4 that includes residue lysine 16. We speculate that this repositioning is incompatible with higher-order nucleosome stacking, which involves contacts of the H4 tail with a neighbouring nucleosome. Our results indicate that pioneer transcription factors can use binding energy to initiate chromatin opening, and thereby facilitate nucleosome remodelling and subsequent transcription.


  • Organizational Affiliation

    Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2
A, E
136Homo sapiensMutation(s): 1 
Gene Names: HIST2H3AHIST2H3CH3F2H3FMHIST2H3D
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Find proteins for Q71DI3 (Homo sapiens)
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PHAROS:  Q71DI3
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UniProt GroupQ71DI3
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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 1-B/E
C, G
151Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFA
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Find proteins for P04908 (Homo sapiens)
Explore P04908 
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PHAROS:  P04908
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UniProt GroupP04908
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-K
D, H
126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BKH2BFTHIRIP1
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Find proteins for O60814 (Homo sapiens)
Explore O60814 
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PHAROS:  O60814
GTEx:  ENSG00000197903 
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (147-MER)147synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (147-MER)147synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilGermany693023
European Molecular Biology OrganizationGermanyALTF-949-2016
Volkswagen FoundationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-13
    Changes: Database references