24MQ | pdb_000024mq

Cryo-EM structure of Arabidopsis H3-H4 octasome

PDB DOI: https://doi.org/10.2210/pdb24MQ/pdb
EM Map EMD-69668: EMDB EMDataResource

Classification: NUCLEAR PROTEIN
Organism(s): synthetic construct, Arabidopsis thaliana
Expression System: Triticum aestivum
Mutation(s): No

Deposited: 2026-03-11 Released: 2026-10-07
Deposition Author(s): Haga, J., Takasuka, T.E.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.82 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 24MQ

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

Literature

Structures of the Arabidopsis nucleosome and H3-H4 octasome assebmled in a wheat germ cell-free co-expression chromatin assembly system

Haga, J., Banko, P., Okimune, K., Azuma, T., Terashi, G., Morishita, R., Kita, S., Maenaka, K., Kihara, D., Takasuka, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 451.67 kDa
Atom Count: 9,388
Modeled Residue Count: 806
Deposited Residue Count: 2,072
Unique protein chains: 2
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	C [auth A], E [auth C], G [auth E], I [auth G]	136	Arabidopsis thaliana	Mutation(s): 0 Gene Names: HTR2, At1g09200, T12M4.9, HTR3, At3g27360, K1G2.8, HTR13, At5g10390, F12B17_260, HTR9... HTR2, At1g09200, T12M4.9, HTR3, At3g27360, K1G2.8, HTR13, At5g10390, F12B17_260, HTR9, At5g10400, F12B17_250, HTR1, At5g65360, MNA5.9
UniProt
Find proteins for P59226 (Arabidopsis thaliana) Explore P59226 Go to UniProtKB: P59226
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P59226
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	D [auth B], F [auth D], H [auth F], J [auth H]	103	Arabidopsis thaliana	Mutation(s): 0 Gene Names: At1g07660, F24B9.25, At1g07820, F24B9.8, At2g28740, F8N16.2, T11P11.4, At3g45930, F16L2_140, At3g46320... At1g07660, F24B9.25, At1g07820, F24B9.8, At2g28740, F8N16.2, T11P11.4, At3g45930, F16L2_140, At3g46320, F18L15.40, At3g53730, F5K20_30, At5g59690, MTH12.10, At5g59970, MMN10.22
UniProt
Find proteins for P59259 (Arabidopsis thaliana) Explore P59259 Go to UniProtKB: P59259
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P59259
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 1
DNA (Widom 601)	A [auth J]	558	synthetic construct
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA (Widom 601)	B [auth I]	558	synthetic construct
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.82 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	v4.7.1
MODEL REFINEMENT	PHENIX	1.21.2_5419
MODEL REFINEMENT	Coot

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	Japan	G-2025-2-039

Revision History (Full details and data files)

Version 1.0: 2026-10-07
Type: Initial release