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- EMDB-62048: Cryo-EM structure of Arabidopsis thaliana H2A.W-H3.3-nucleosome w... -

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Basic information

Entry
Database: EMDB / ID: EMD-62048
TitleCryo-EM structure of Arabidopsis thaliana H2A.W-H3.3-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry)
Map datamap
Sample
  • Complex: Arabidopsis thaliana H2A.W-H3.3-nucleosome with Arabidopsis native 147bp DNA 15.2.2
    • Protein or peptide: Histone H3.3
    • Protein or peptide: Histone H4
    • Protein or peptide: Probable histone H2A.7
    • Protein or peptide: Histone H2B.1
    • DNA: 15.2.2 DNA (147-MER)
    • DNA: 15.2.2 DNA (147-MER)
Keywordsnucleosome / histone / H2A.W / H3.3 / Arabidopsis / NUCLEAR PROTEIN/DNA / NUCLEAR PROTEIN-DNA complex
Function / homology
Function and homology information


rDNA protrusion / heterochromatin organization / thylakoid / response to water deprivation / plant-type vacuole / plasmodesma / plastid / pericentric heterochromatin / heterochromatin / chloroplast ...rDNA protrusion / heterochromatin organization / thylakoid / response to water deprivation / plant-type vacuole / plasmodesma / plastid / pericentric heterochromatin / heterochromatin / chloroplast / structural constituent of chromatin / peroxisome / nucleosome / protein heterodimerization activity / chromatin binding / nucleolus / DNA binding / extracellular region / nucleus / plasma membrane / cytosol
Similarity search - Function
: / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A ...: / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / 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 domain / Histone-fold
Similarity search - Domain/homology
Histone H3.3 / Histone H4 / Probable histone H2A.7 / Histone H2B.1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsWang Y / Dong A
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930017 China
CitationJournal: To Be Published
Title: Functional redundancy of core histone H2A and its variants in Arabidopsis
Authors: Wang Y / Dong A
History
DepositionOct 21, 2024-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62048.png

Downloads & links

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Map

FileDownload / File: emd_62048.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.432 Å		1.07 Å/pix.
x 256 pix.
= 274.432 Å		1.07 Å/pix.
x 256 pix.
= 274.432 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.072 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.46859258 - 1.3995342
Average (Standard dev.)-0.0039506764 (±0.05079715)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.432 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62048_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: map sharp

Fileemd_62048_additional_1.map
Annotationmap_sharp
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: map half A

Fileemd_62048_half_map_1.map
Annotationmap_half_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: map half B

Fileemd_62048_half_map_2.map
Annotationmap_half_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Arabidopsis thaliana H2A.W-H3.3-nucleosome with Arabidopsis nativ...

EntireName: Arabidopsis thaliana H2A.W-H3.3-nucleosome with Arabidopsis native 147bp DNA 15.2.2
Components
  • Complex: Arabidopsis thaliana H2A.W-H3.3-nucleosome with Arabidopsis native 147bp DNA 15.2.2
    • Protein or peptide: Histone H3.3
    • Protein or peptide: Histone H4
    • Protein or peptide: Probable histone H2A.7
    • Protein or peptide: Histone H2B.1
    • DNA: 15.2.2 DNA (147-MER)
    • DNA: 15.2.2 DNA (147-MER)

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Supramolecule #1: Arabidopsis thaliana H2A.W-H3.3-nucleosome with Arabidopsis nativ...

SupramoleculeName: Arabidopsis thaliana H2A.W-H3.3-nucleosome with Arabidopsis native 147bp DNA 15.2.2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Histone H3.3

MacromoleculeName: Histone H3.3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 15.440144 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PTTGGVKKPH RYRPGTVALR EIRKYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSHA VLALQEAAEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.3

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 11.436467 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK IFLENVIRDA VTYTEHARRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Probable histone H2A.7

MacromoleculeName: Probable histone H2A.7 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 15.997942 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MESTGKVKKA FGGRKPPGAP KTKSVSKSMK AGLQFPVGRI TRFLKKGRYA QRLGGGAPVY MAAVLEYLAA EVLELAGNAA RDNKKSRII PRHLLLAIRN DEELGKLLSG VTIAHGGVLP NINSVLLPKK SATKPAEEKA TKSPVKSPKK A

UniProtKB: Probable histone H2A.7

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Macromolecule #4: Histone H2B.1

MacromoleculeName: Histone H2B.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 16.439291 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAPRAEKKPA EKKTAAERPV EENKAAEKAP AEKKPKAGKK LPPKEAGDKK KKRSKKNVET YKIYIFKVLK QVHPDIGISS KAMGIMNSF INDIFEKLAQ ESSKLARYNK KPTITSREIQ TAVRLVLPGE LAKHAVSEGT KAVTKFTSS

UniProtKB: Histone H2B.1

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Macromolecule #5: 15.2.2 DNA (147-MER)

MacromoleculeName: 15.2.2 DNA (147-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 45.071871 KDa
SequenceString: (DA)(DC)(DC)(DT)(DT)(DT)(DA)(DT)(DT)(DG) (DA)(DC)(DT)(DC)(DC)(DA)(DT)(DA)(DA)(DT) (DT)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT) (DG)(DA)(DG)(DC)(DG)(DG)(DC)(DT)(DC)(DG) (DA) (DT)(DT)(DC)(DA)(DA)(DC) ...String:
(DA)(DC)(DC)(DT)(DT)(DT)(DA)(DT)(DT)(DG) (DA)(DC)(DT)(DC)(DC)(DA)(DT)(DA)(DA)(DT) (DT)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT) (DG)(DA)(DG)(DC)(DG)(DG)(DC)(DT)(DC)(DG) (DA) (DT)(DT)(DC)(DA)(DA)(DC)(DT)(DG) (DT)(DC)(DA)(DA)(DT)(DA)(DA)(DC)(DT)(DT) (DC)(DA) (DA)(DA)(DT)(DG)(DA)(DA)(DG) (DC)(DA)(DA)(DG)(DA)(DG)(DC)(DC)(DT)(DT) (DA)(DT)(DC) (DG)(DT)(DA)(DT)(DT)(DC) (DT)(DC)(DC)(DG)(DC)(DA)(DC)(DG)(DA)(DT) (DG)(DG)(DT)(DG) (DC)(DT)(DT)(DT)(DA) (DA)(DT)(DC)(DC)(DA)(DC)(DC)(DG)(DC)(DA) (DA)(DC)(DT)(DT)(DT) (DC)(DC)(DT)(DC) (DT)(DT)(DT)(DA)(DA)(DT)(DA)(DA)(DA)(DG) (DG)(DC)(DA)(DC)(DA)(DA) (DG)(DC)(DA) (DT)(DT)(DA)(DA)

GENBANK: GENBANK: AL161580.2

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Macromolecule #6: 15.2.2 DNA (147-MER)

MacromoleculeName: 15.2.2 DNA (147-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 45.654219 KDa
SequenceString: (DT)(DT)(DA)(DA)(DT)(DG)(DC)(DT)(DT)(DG) (DT)(DG)(DC)(DC)(DT)(DT)(DT)(DA)(DT)(DT) (DA)(DA)(DA)(DG)(DA)(DG)(DG)(DA)(DA) (DA)(DG)(DT)(DT)(DG)(DC)(DG)(DG)(DT)(DG) (DG) (DA)(DT)(DT)(DA)(DA)(DA) ...String:
(DT)(DT)(DA)(DA)(DT)(DG)(DC)(DT)(DT)(DG) (DT)(DG)(DC)(DC)(DT)(DT)(DT)(DA)(DT)(DT) (DA)(DA)(DA)(DG)(DA)(DG)(DG)(DA)(DA) (DA)(DG)(DT)(DT)(DG)(DC)(DG)(DG)(DT)(DG) (DG) (DA)(DT)(DT)(DA)(DA)(DA)(DG)(DC) (DA)(DC)(DC)(DA)(DT)(DC)(DG)(DT)(DG)(DC) (DG)(DG) (DA)(DG)(DA)(DA)(DT)(DA)(DC) (DG)(DA)(DT)(DA)(DA)(DG)(DG)(DC)(DT)(DC) (DT)(DT)(DG) (DC)(DT)(DT)(DC)(DA)(DT) (DT)(DT)(DG)(DA)(DA)(DG)(DT)(DT)(DA)(DT) (DT)(DG)(DA)(DC) (DA)(DG)(DT)(DT)(DG) (DA)(DA)(DT)(DC)(DG)(DA)(DG)(DC)(DC)(DG) (DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG) (DT)(DC)(DA)(DA)(DT)(DT)(DA)(DT)(DG)(DG) (DA)(DG)(DT)(DC)(DA)(DA) (DT)(DA)(DA) (DA)(DG)(DG)(DT)

GENBANK: GENBANK: AL161580.2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.9 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 165777
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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