Download MendeleyStructural and functional interrelationships of histone H2A with its variants H2A.Z and H2A.W in Arabidopsis
Wang, Y., Dong, A.(2025) Structure
9K43 | pdb_00009k43
Cryo-EM structure of Arabidopsis thaliana H2A.Z-nucleosome with 147bp Widom 601 DNA (C2 symmetry)
- PDB DOI: https://doi.org/10.2210/pdb9K43/pdb
- EM Map EMD-62042: EMDB EMDataResource
- Classification: NUCLEAR PROTEIN/DNA
- Organism(s): Arabidopsis thaliana
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2024-10-21 Released: 2025-05-14
- Funding Organization(s): National Natural Science Foundation of China (NSFC)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 2.87 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Histone H3.1 | 136 | Arabidopsis thaliana | Mutation(s): 0 Gene Names: |  | |
UniProt | |||||
Find proteins for P59226 (Arabidopsis thaliana) Explore P59226 Go to UniProtKB: P59226 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P59226 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Histone H4 | 103 | Arabidopsis thaliana | Mutation(s): 0 Gene Names: At1g07660, F24B9.25, At1g07820, F24B9.8, At2g28740, F8N16.2, T11P11.4, At3g45930, F16L2_140, At3g46320... |  | |
UniProt | |||||
Find proteins for P59259 (Arabidopsis thaliana) Explore P59259 Go to UniProtKB: P59259 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P59259 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Probable histone H2A variant 3 | 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 Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9C944 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Histone H2B.1 | 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 Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9LQQ4 | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| Widom 601 DNA (147-MER) | 147 | Arabidopsis thaliana |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by:
(by identity cutoff) | 3D Structure
Entity ID: 6 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| Widom 601 DNA (147-MER) | 147 | Arabidopsis thaliana |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 2.87 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
| Task | Software Package | Version |
|---|---|---|
| MODEL REFINEMENT | PHENIX | 1.20.1_4487: |
| RECONSTRUCTION | cryoSPARC | 4.3 |
Entry History & Funding Information
Deposition Data
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Natural Science Foundation of China (NSFC) | China | 31930017 |
Revision History (Full details and data files)
- Version 1.0: 2025-05-14
Type: Initial release
