6T7D

Structure of human Sox11 transcription factor in complex with a nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 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

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

  • 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. ...

    '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. patrick.cramer@mpibpc.mpg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2AE136Homo sapiensMutation(s): 0 
Gene Names: HIST2H3AHIST2H3CH3F2H3FMHIST2H3DH3C15H3C14H3C13
Find proteins for Q71DI3 (Homo sapiens)
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PHAROS  Q71DI3
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4BF103Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
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PHAROS  P62805
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/ECG151Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFAH2AC4H2AC8
Find proteins for P04908 (Homo sapiens)
Explore P04908 
Go to UniProtKB:  P04908
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PHAROS  P04908
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-KDH126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BKH2BFTHIRIP1H2BC12
Find proteins for O60814 (Homo sapiens)
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PHAROS  O60814
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  • Reference Sequence
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription factor SOX-11K109Homo sapiensMutation(s): 0 
Gene Names: SOX11
Find proteins for P35716 (Homo sapiens)
Explore P35716 
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PHAROS  P35716
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (151-MER)I151synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (151-MER)J151synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 

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