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- EMDB-18060: CryoEM structure of canonical rice nucleosome core particle -

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Basic information

Entry
Database: EMDB / ID: EMD-18060
TitleCryoEM structure of canonical rice nucleosome core particle
Map data
Sample
  • Complex: Rice canonical nucleosome core particle with widom 601 DNA sequence
    • Protein or peptide: Histone H2A.2
    • Protein or peptide: Histone H2B.4
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • DNA: WIDOM 601
    • DNA: WIDOM 601
KeywordsHistone / Nucleosome core particle / Rice nucleosome / chromatin / DNA BINDING PROTEIN
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / nucleus
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 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
Histone H2B.4 / Histone H3.2 / Probable histone H2A.2
Similarity search - Component
Biological speciesOryza (plant) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsSotelo-Parrilla P / Hari Sundar G V / Raju S / Jha S / Gireesh A / Gut F / Vinothkumar KR / Berger F / Shivaprasad PV / Jeyaprakash AA
Funding supportEuropean Union, United Kingdom, India, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)101054950European Union
Wellcome Trust United Kingdom
Department of Biotechnology (DBT, India) India
CitationJournal: Nat Plants / Year: 2025
Title: An Oryza-specific histone H4 variant predisposes H4 lysine 5 acetylation to modulate salt stress responses.
Authors: Vivek Hari-Sundar Gandhivel / Paula Sotelo-Parrilla / Steffi Raju / Shaileshanand Jha / Anjitha Gireesh / Chitthavalli Y Harshith / Fabian Gut / Kutti R Vinothkumar / Frédéric Berger / A ...Authors: Vivek Hari-Sundar Gandhivel / Paula Sotelo-Parrilla / Steffi Raju / Shaileshanand Jha / Anjitha Gireesh / Chitthavalli Y Harshith / Fabian Gut / Kutti R Vinothkumar / Frédéric Berger / A Arockia Jeyaprakash / P V Shivaprasad /
Abstract: Paralogous variants of canonical histones guide accessibility to DNA and function as additional layers of genome regulation. Across eukaryotes, the mechanism of action and functional significance of ...Paralogous variants of canonical histones guide accessibility to DNA and function as additional layers of genome regulation. Across eukaryotes, the mechanism of action and functional significance of several variants of core histones are well known except those of histone H4. Here we show that a variant of H4 (H4.V) expressing tissue-specifically among Oryza members mediated specific epigenetic changes contributing to salt tolerance. H4.V was incorporated into specific heterochromatic sites, where it blocked the deposition of active histone marks. Stress-dependent redistribution of H4.V enabled the incorporation of acetylated H4 lysine 5 (H4K5ac) in the gene bodies. The misexpression of H4.V led to defects in reproductive development and in mounting salt stress responses. H4.V formed homotypic nucleosomes and mediated these alterations by conferring distinct molecular properties to the nucleosomes, as seen with cryo electron microscopy structures and biochemical assays. These results reveal not only an H4 variant among plants but also a chromatin regulation that might have contributed to the adaptation of semi-aquatic Oryza members.
History
DepositionJul 30, 2023-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18060.png

Downloads & links

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Map

FileDownload / File: emd_18060.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 300 pix.
= 218.1 Å		0.73 Å/pix.
x 300 pix.
= 218.1 Å		0.73 Å/pix.
x 300 pix.
= 218.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.7949106 - 2.9558914
Average (Standard dev.)0.0045020105 (±0.07372512)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 218.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18060_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Additional map: #1

Fileemd_18060_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_18060_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_18060_half_map_2.map
Projections & Slices
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Sample components

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Entire : Rice canonical nucleosome core particle with widom 601 DNA sequence

EntireName: Rice canonical nucleosome core particle with widom 601 DNA sequence
Components
  • Complex: Rice canonical nucleosome core particle with widom 601 DNA sequence
    • Protein or peptide: Histone H2A.2
    • Protein or peptide: Histone H2B.4
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • DNA: WIDOM 601
    • DNA: WIDOM 601

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Supramolecule #1: Rice canonical nucleosome core particle with widom 601 DNA sequence

SupramoleculeName: Rice canonical nucleosome core particle with widom 601 DNA sequence
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryza (plant)

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Macromolecule #1: Histone H2A.2

MacromoleculeName: Histone H2A.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryza (plant)
Molecular weightTheoretical: 13.999209 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAGRGKAIGS GAAKKAMSRS SKAGLQFPVG RIARFLKAGK YAERVGAGAP VYLAAVLEYL AAEVLELAGN AARDNKKTRI VPRHIQLAV RNDEELSRLL GTVTIASGGV MPNIHNLLLP KKAGGSAKAA AGDDDN

UniProtKB: Probable histone H2A.2

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Macromolecule #2: Histone H2B.4

MacromoleculeName: Histone H2B.4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryza (plant)
Molecular weightTheoretical: 16.539408 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAPKAEKKPA AKKPAEEEPA AEKAEKAPAG KKPKAEKRLP AGKAEKGSGE GKKAGRKKAK KSVETYKIYI FKVLKQVHPD IGISSKAMS IMNSFINDIF EKLAGESAKL ARYNKKPTIT SREIQTSVRL VLPGELAKHA VSEGTKAVTK FTSA

UniProtKB: Histone H2B.4

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Macromolecule #3: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryza (plant)
Molecular weightTheoretical: 15.300968 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RFRPGTVALR EIRKYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VAALQEAAEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.2

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Macromolecule #4: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryza (plant)
Molecular weightTheoretical: 11.436467 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK IFLENVIRDA VTYTEHARRK TVTAMDVVY ALKRQGRTLY GFGG

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Macromolecule #5: WIDOM 601

MacromoleculeName: WIDOM 601 / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.330867 KDa
SequenceString: (DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DG)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC) ...String:
(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DG)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC) (DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA) (DA)(DA) (DA)(DC)(DG)(DC)(DG)(DG)(DG) (DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG) (DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT) (DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG) (DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA) (DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG) (DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC) (DG)(DG)(DG)(DA)(DT)(DT) (DC)(DT)(DC) (DC)(DA)(DG)

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Macromolecule #6: WIDOM 601

MacromoleculeName: WIDOM 601 / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.801535 KDa
SequenceString: (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT) ...String:
(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DC)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DT)(DG)

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 140877
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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