6YOV

OCT4-SOX2-bound nucleosome - SHL+6


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanisms of OCT4-SOX2 motif readout on nucleosomes.

Michael, A.K.Grand, R.S.Isbel, L.Cavadini, S.Kozicka, Z.Kempf, G.Bunker, R.D.Schenk, A.D.Graff-Meyer, A.Pathare, G.R.Weiss, J.Matsumoto, S.Burger, L.Schubeler, D.Thoma, N.H.

(2020) Science 368: 1460-1465

  • DOI: https://doi.org/10.1126/science.abb0074
  • Primary Citation of Related Structures:  
    6T90, 6T93, 6YOV

  • PubMed Abstract: 

    Transcription factors (TFs) regulate gene expression through chromatin where nucleosomes restrict DNA access. To study how TFs bind nucleosome-occupied motifs, we focused on the reprogramming factors OCT4 and SOX2 in mouse embryonic stem cells. We determined TF engagement throughout a nucleosome at base-pair resolution in vitro, enabling structure determination by cryo-electron microscopy at two preferred positions. Depending on motif location, OCT4 and SOX2 differentially distort nucleosomal DNA. At one position, OCT4-SOX2 removes DNA from histone H2A and histone H3; however, at an inverted motif, the TFs only induce local DNA distortions. OCT4 uses one of its two DNA-binding domains to engage DNA in both structures, reading out a partial motif. These findings explain site-specific nucleosome engagement by the pluripotency factors OCT4 and SOX2, and they reveal how TFs distort nucleosomes to access chromatinized motifs.


  • Organizational Affiliation

    Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland. nicolas.thoma@fmi.ch dirk@fmi.ch.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1139Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P68431 (Homo sapiens)
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Go to UniProtKB:  P68431
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UniProt GroupP68431
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4105Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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UniProt GroupP62805
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/E
C, G
133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFA
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Find proteins for P04908 (Homo sapiens)
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UniProt GroupP04908
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-J
D, H
128Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFR
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Find proteins for P06899 (Homo sapiens)
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PHAROS:  P06899
GTEx:  ENSG00000124635 
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UniProt GroupP06899
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1137Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4106Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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UniProt GroupP62805
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Green fluorescent protein,POU domain, class 5, transcription factor 1631Aequorea victoriaHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: GFPPOU5F1OCT3OCT4OTF3
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Find proteins for Q01860 (Homo sapiens)
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GTEx:  ENSG00000204531 
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UniProt GroupsP42212Q01860
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor SOX-2105Homo sapiensMutation(s): 0 
Gene Names: SOX2
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Find proteins for P48431 (Homo sapiens)
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GTEx:  ENSG00000181449 
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (142-MER)
I, J
300synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandCRSII3_160734/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2020-05-13
    Changes: Database references
  • Version 1.2: 2020-07-08
    Changes: Database references