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- PDB-9k3z: Cryo-EM structure of Arabidopsis thaliana H2A.Z-nucleosome with A... -

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Basic information

Entry
Database: PDB / ID: 9k3z
TitleCryo-EM structure of Arabidopsis thaliana H2A.Z-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry)
Components
  • (15.2.2 DNA (147- ...) x 2
  • Histone H2B.1
  • Histone H3.1
  • Histone H4
  • Probable histone H2A variant 3
KeywordsNUCLEAR PROTEIN/DNA / nucleosome / histone / H2A.Z / Arabidopsis / NUCLEAR PROTEIN-DNA complex
Function / homology
Function and homology information


chromocenter / thylakoid / response to water deprivation / plasmodesma / plant-type vacuole / plastid / response to temperature stimulus / chloroplast / structural constituent of chromatin / nucleosome ...chromocenter / thylakoid / response to water deprivation / plasmodesma / plant-type vacuole / plastid / response to temperature stimulus / chloroplast / structural constituent of chromatin / nucleosome / peroxisome / regulation of gene expression / protein heterodimerization activity / nucleolus / DNA binding / extracellular region / nucleus / plasma membrane / cytosol
Similarity search - Function
: / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A ...: / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA (> 100) / Histone H3.1 / Histone H4 / Probable histone H2A variant 3 / Histone H2B.1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsWang, Y. / Dong, A.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930017 China
CitationJournal: Structure / Year: 2025
Title: Structural and functional interrelationships of histone H2A with its variants H2A.Z and H2A.W in Arabidopsis.
Authors: Youchao Wang / Jiabing Wu / Shuoming Yang / Xiang Li / Jiachen Wang / Qinghe Lv / Xiaoyu Zhu / Guoliang Lu / Jinru Zhang / Wen-Hui Shen / Bing Liu / Jinzhong Lin / Aiwu Dong /
Abstract: Multiple histone H2A variants are known in eukaryotes. However, the functional relationship between H2A and its variants in plants remains largely obscure. Using CRISPR-Cas9 editing, we generated a ...Multiple histone H2A variants are known in eukaryotes. However, the functional relationship between H2A and its variants in plants remains largely obscure. Using CRISPR-Cas9 editing, we generated a mutant lacking four H2A isoforms in Arabidopsis and analyzed the functional and structural relationships between H2A, H2A.Z, and H2A.W. RNA sequencing and phenotype analyses revealed mild changes in gene transcription and plant development in mutants lacking H2A, H2A.Z, or H2A.W compared with the wild-type plants. Chromatin immunoprecipitation sequencing analysis showed that H2A can substitute for both H2A.Z and H2A.W across the genome, including in euchromatin and heterochromatin regions. However, H2A.Z replaced both H2A and H2A.W primarily within the euchromatin regions. By using DNA and histones from Arabidopsis, we constructed nucleosomes containing H2A, H2A.Z, or H2A.W and resolved their cryogenic electron microscopy (cryo-EM) structures at near-atomic resolution. Collectively, the results reveal the structural similarity and functional redundancy of H2A and its variants in Arabidopsis.
History
DepositionOct 21, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.1
B: Histone H4
C: Probable histone H2A variant 3
D: Histone H2B.1
E: Histone H3.1
F: Histone H4
G: Probable histone H2A variant 3
H: Histone H2B.1
I: 15.2.2 DNA (147-MER)
J: 15.2.2 DNA (147-MER)


Theoretical massNumber of molelcules
Total (without water)205,68310
Polymers205,68310
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3.1


Mass: 15300.968 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress)
Gene: HTR2, At1g09200, T12M4.9, HTR3, At3g27360, K1G2.8, HTR13, At5g10390, F12B17_260, HTR9, At5g10400, F12B17_250, HTR1, At5g65360, MNA5.9
Production host: Escherichia coli (E. coli) / References: UniProt: P59226
#2: Protein Histone H4


Mass: 11436.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress)
Gene: 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
Production host: Escherichia coli (E. coli) / References: UniProt: P59259
#3: Protein Probable histone H2A variant 3 / H2A.F/Z 3 / HTA9


Mass: 14301.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g52740, F14G24.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9C944
#4: Protein Histone H2B.1 / HTB1


Mass: 16439.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g07790, F24B9.10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LQQ4

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15.2.2 DNA (147- ... , 2 types, 2 molecules IJ

#5: DNA chain 15.2.2 DNA (147-MER)


Mass: 45071.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: GenBank: 4584519
#6: DNA chain 15.2.2 DNA (147-MER)


Mass: 45654.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: GenBank: 4584519

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Arabidopsis thaliana H2A.Z-nucleosome with Arabidopsis native 147bp DNA 15.2.2
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 900 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIX1.20.1_4487:model refinement
3EPUimage acquisition
13cryoSPARC4.33D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 192738 / Symmetry type: POINT

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