9K45 | pdb_00009k45

Cryo-EM structure of Arabidopsis thaliana H2A.Z-H3.3-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry)

• PDB DOI: https://doi.org/10.2210/pdb9K45/pdb
• EM Map EMD-62046: EMDB EMDataResource
• NAKB: 9K45

• Classification: NUCLEAR PROTEIN/DNA
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-21 Released: 2025-11-12 
• Deposition Author(s): Wang, Y., Dong, A.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.71 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Functional redundancy of core histone H2A and its variants in Arabidopsis

Wang, Y., Dong, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 205.96 kDa 
• Atom Count: 11,830 
• Modeled Residue Count: 1,034 
• Deposited Residue Count: 1,336 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.3	A, E	136	Arabidopsis thaliana	Mutation(s): 0  Gene Names: HTR4, At4g40030, T5J17.200, HTR5, At4g40040, T5J17.210, HTR8, At5g10980, T30N20_250, T5K6.6
UniProt
Find proteins for P59169 (Arabidopsis thaliana) Explore P59169  Go to UniProtKB:  P59169

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	103	Arabidopsis thaliana	Mutation(s): 0  Gene Names:  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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable histone H2A variant 3	C, G	134	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At1g52740, F14G24.1
UniProt
Find proteins for Q9C944 (Arabidopsis thaliana) Explore Q9C944  Go to UniProtKB:  Q9C944

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B.1	D, H	148	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At1g07790, F24B9.10
UniProt
Find proteins for Q9LQQ4 (Arabidopsis thaliana) Explore Q9LQQ4  Go to UniProtKB:  Q9LQQ4

Entity ID: 5
Molecule	Chains	Length	Organism	Image
15.2.2 DNA (147-MER)	I	147	Arabidopsis thaliana

Entity ID: 6
Molecule	Chains	Length	Organism	Image
15.2.2 DNA (147-MER)	J	147	Arabidopsis thaliana

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.71 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:
RECONSTRUCTION	cryoSPARC	4.3

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Wang, Y., Dong, A.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31930017

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release