6T93

Nucleosome with OCT4-SOX2 motif at SHL-6


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.49 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:  
    6T93, 6T90, 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. We determined TF engagement througho ...

    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. We determined TF engagement throughout a nucleosome at base-pair resolution in vitro, enabling cryo-EM structure determination at two preferred positions. Depending on motif location, OCT4-SOX2 differentially distort nucleosomal DNA. At one position, OCT4-SOX2 removes DNA from Histone H2A/Histone H3 (H2A/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-SOX2 and 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 H3.1AE139Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P68431 (Homo sapiens)
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Go to UniProtKB:  P68431
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PHAROS  P68431
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4BF106Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
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PHAROS  P62805
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/ECG133Homo 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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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-JDH129Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFRH2BC11
Find proteins for P06899 (Homo sapiens)
Explore P06899 
Go to UniProtKB:  P06899
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PHAROS  P06899
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (153-MER)I153synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (153-MER)J153synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.49 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 FoundationSwitzerlandSinergia-CRSII3_160734

Revision History 

  • 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