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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1A139Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P68431 (Homo sapiens)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B105Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/EC, G133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFAH2AC4H2AC8
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-JD, H128Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFRH2BC11
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1E137Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4F106Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Green fluorescent protein,POU domain, class 5, transcription factor 1K631Aequorea victoriaHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: GFPPOU5F1OCT3OCT4OTF3
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription factor SOX-2L105Homo sapiensMutation(s): 0 
Gene Names: SOX2
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Find proteins for P48431 (Homo sapiens)
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (142-MER)I, J300synthetic construct
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Experimental Data & Validation

Experimental Data

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

Structure Validation

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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