6T78

Structure of human Sox11 transcription factor in complex with a short DNA fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

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
  • Structures With Same Primary Citation

  • 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcription factor SOX-11
A, B
109Homo sapiensMutation(s): 0 
Gene Names: SOX11
Find proteins for P35716 (Homo sapiens)
Go to UniProtKB:  P35716
NIH Common Fund Data Resources
PHAROS  P35716
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*TP*TP*GP*TP*TP*TP*AP*TP*TP*TP*TP*GP*TP*T)-3')C, F16synthetic construct
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*CP*AP*AP*AP*AP*TP*AP*AP*AP*CP*AP*AP*TP*A)-3')D, G16synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.13α = 90
b = 106.13β = 90
c = 76.89γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

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