8Q15 | pdb_00008q15

CryoEM structure of canonical rice nucleosome core particle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

An Oryza-specific histone H4 variant predisposes H4 lysine 5 acetylation to modulate salt stress responses.

Gandhivel, V.H.Sotelo-Parrilla, P.Raju, S.Jha, S.Gireesh, A.Harshith, C.Y.Gut, F.Vinothkumar, K.R.Berger, F.Jeyaprakash, A.A.Shivaprasad, P.V.

(2025) Nat Plants 11: 790-807

  • DOI: https://doi.org/10.1038/s41477-025-01974-2
  • Primary Citation of Related Structures:  
    8Q15, 8Q16

  • PubMed Abstract: 

    Paralogous variants of canonical histones guide accessibility to DNA and function as additional layers of genome regulation. Across eukaryotes, the mechanism of action and functional significance of several variants of core histones are well known except those of histone H4. Here we show that a variant of H4 (H4.V) expressing tissue-specifically among Oryza members mediated specific epigenetic changes contributing to salt tolerance. H4.V was incorporated into specific heterochromatic sites, where it blocked the deposition of active histone marks. Stress-dependent redistribution of H4.V enabled the incorporation of acetylated H4 lysine 5 (H4K5ac) in the gene bodies. The misexpression of H4.V led to defects in reproductive development and in mounting salt stress responses. H4.V formed homotypic nucleosomes and mediated these alterations by conferring distinct molecular properties to the nucleosomes, as seen with cryo electron microscopy structures and biochemical assays. These results reveal not only an H4 variant among plants but also a chromatin regulation that might have contributed to the adaptation of semi-aquatic Oryza members.


  • Organizational Affiliation
    • National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore, India.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A.2
A, B
135OryzaMutation(s): 0 
Gene Names: OsI_025469
UniProt
Find proteins for A2YMC6 (Oryza sativa subsp. indica)
Explore A2YMC6 
Go to UniProtKB:  A2YMC6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2YMC6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B.4
C, D
153OryzaMutation(s): 0 
Gene Names: H2B.4OsI_000388
UniProt
Find proteins for A2WKP5 (Oryza sativa subsp. indica)
Explore A2WKP5 
Go to UniProtKB:  A2WKP5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2WKP5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2
E, F
136OryzaMutation(s): 0 
Gene Names: OsI_019426OsI_021009OsI_021012OsI_033964
UniProt
Find proteins for A2Y533 (Oryza sativa subsp. indica)
Explore A2Y533 
Go to UniProtKB:  A2Y533
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2Y533
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
G, H
103OryzaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains LengthOrganismImage
WIDOM 601146synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains LengthOrganismImage
WIDOM 601146synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union101054950
Wellcome TrustUnited Kingdom--
Department of Biotechnology (DBT, India)India--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-04-16
    Changes: Data collection, Database references
  • Version 1.2: 2025-04-23
    Changes: Data collection, Database references
  • Version 1.3: 2025-05-07
    Changes: Data collection, Database references
  • Version 1.4: 2025-07-02
    Changes: Data collection