Skip to main content

 38BO | pdb_000038bo

Arabidopsis H2AXa containing nucleosome, Parallel stack


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 38BO

This is version 1.0 of the entry. See complete history. 

Literature

Molecular Architecture of the H2AX-Containing Nucleosome from Arabidopsis.

Panigrahi, R., Edwards, R., Agbagba, N., Glover, M.

(2026) Cells 15

  • DOI: https://doi.org/10.3390/cells15191795
  • Primary Citation Related Structures: 
    37ZO, 38BO

  • PubMed Abstract: 

    Nucleosomes integrate diverse histone variants to organize chromatin and coordinate genome maintenance. In plants, the structural interplay between replication-associated histones and DNA damage-responsive histone variants remains poorly understood. Here, we determine cryogenic electron microscopy structures of an Arabidopsis thaliana ( At ) nucleosome containing the replication-associated histones H2B.6 and H3.1 together with the DNA damage-responsive variant H2AXa. The mononucleosome structure, resolved at 2.73 Å, preserves the canonical nucleosome architecture. Unexpectedly, the reconstituted mononucleosomes formed defined higher-order assemblies in the absence of linker DNA or chemical crosslinking. Two distinct nucleosome-nucleosome arrangements, parallel and right offset, were identified. The right offset closely resembles the human counterpart, whereas the parallel arrangement exhibits slight displacement of H2B structural elements at the inter-nucleosomal interface. Together these structures reveal how a distinct histone composition preserves the canonical nucleosome architecture while supporting multiple defined modes of nucleosome packing, providing structural insights into conserved and divergent features of H2AX-containing chromatin organization across plants and animals.


  • Organizational Affiliation: 
    • Department of Human Biosciences, Memorial University of Newfoundland, St John's, NL A1C 5S7, Canada.

Macromolecule Content 

  • Total Structure Weight: 426.76 kDa 
  • Atom Count: 23,632 
  • Modeled Residue Count: 2,074 
  • Deposited Residue Count: 2,832 
  • Unique protein chains: 4
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Core Histone H2A/H2B/H3 domain-containing proteinA,
E,
K [auth L],
O [auth P]
152Arabidopsis thalianaMutation(s): 0 
Gene Names: AABB24_003545
UniProt
Find proteins for A0ABD2V7Q4 (Solanum stoloniferum)
Explore A0ABD2V7Q4 
Go to UniProtKB:  A0ABD2V7Q4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ABD2V7Q4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H4B,
F,
L [auth M],
P [auth Q]
103Arabidopsis thalianaMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P59259 (Arabidopsis thaliana)
Explore P59259 
Go to UniProtKB:  P59259
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59259
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable histone H2AXaC,
G,
M [auth N],
Q [auth R]
158Arabidopsis thalianaMutation(s): 0 
Gene Names: At1g08880, F7G19.24
UniProt
Find proteins for O04848 (Arabidopsis thaliana)
Explore O04848 
Go to UniProtKB:  O04848
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO04848
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2BD,
H,
N [auth O],
R [auth S]
150Arabidopsis thalianaMutation(s): 0 
Gene Names: At3g45980
UniProt
Find proteins for Q0WT91 (Arabidopsis thaliana)
Explore Q0WT91 
Go to UniProtKB:  Q0WT91
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0WT91
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (145-MER)I,
S [auth X]
145synthetic construct
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (145-MER)J,
T [auth Y]
145synthetic construct
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX2.0_5936
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-28
    Type: Initial release