9D3K | pdb_00009d3k

Two Dsup molecules in complex with the nucleosome open from both sides


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 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

Structural basis of nucleosome recognition by the conserved Dsup and HMGN nucleosome-binding motif.

Alegrio-Louro, J.Cruz-Becerra, G.Kassavetis, G.A.Kadonaga, J.T.Leschziner, A.E.

(2025) Genes Dev 39: 1155-1161

  • DOI: https://doi.org/10.1101/gad.352720.125
  • Primary Citation of Related Structures:  
    9D3K, 9D3L, 9D3M, 9D3N, 9D3O, 9D3P, 9D3Q, 9D3R, 9D3S, 9D3T

  • PubMed Abstract: 

    The tardigrade damage suppressor (Dsup) and vertebrate high-mobility group N (HMGN) proteins bind specifically to nucleosomes via a conserved motif whose structure has not been experimentally determined. Here we used cryo-EM to show that both proteins bind to the nucleosome acidic patch via analogous arginine anchors with one molecule bound to each face of the nucleosome. We additionally used the natural promoter-containing 5S rDNA sequence for structural analysis of the nucleosome. These structures of an ancient nucleosome-binding motif suggest that there is an untapped realm of proteins with a related mode of binding to chromatin.


  • Organizational Affiliation
    • Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, USA.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2
A, E
95Homo sapiensMutation(s): 0 
Gene Names: H3C15HIST2H3AH3C14H3F2H3FMHIST2H3CH3C13HIST2H3D
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Find proteins for Q71DI3 (Homo sapiens)
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PHAROS:  Q71DI3
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UniProt GroupQ71DI3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
79Homo 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 2-A
C, G
102Homo sapiensMutation(s): 0 
Gene Names: H2AC18H2AFOHIST2H2AAHIST2H2AA3H2AC19HIST2H2AA4
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Find proteins for Q6FI13 (Homo sapiens)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-M90Homo sapiensMutation(s): 0 
Gene Names: H2BC14H2BFEHIST1H2BM
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Find proteins for Q99879 (Homo sapiens)
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GTEx:  ENSG00000273703 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-M90Homo sapiensMutation(s): 0 
Gene Names: H2BC14H2BFEHIST1H2BM
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GTEx:  ENSG00000273703 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Damage suppressor proteinK [auth L],
L [auth K]
8Ramazzottius varieornatusMutation(s): 0 
Gene Names: DsupRvY_17224
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Entity ID: 6
MoleculeChains LengthOrganismImage
601 DNAI [auth J]94synthetic construct
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Entity ID: 7
MoleculeChains LengthOrganismImage
601 DNAJ [auth I]94synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM145296
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM118060

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release
  • Version 1.1: 2025-10-15
    Changes: Data collection, Database references