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- PDB-8q15: CryoEM structure of canonical rice nucleosome core particle -

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Basic information

Entry
Database: PDB / ID: 8q15
TitleCryoEM structure of canonical rice nucleosome core particle
Components
  • (WIDOM 601) x 2
  • Histone H2A.2
  • Histone H2B.4
  • Histone H3.2
  • Histone H4
KeywordsDNA BINDING PROTEIN / Histone / Nucleosome core particle / Rice nucleosome / chromatin
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
DNA / DNA (> 10) / DNA (> 100) / Histone H2B.4 / Histone H3.2 / Probable histone H2A.2
Similarity search - Component
Biological speciesOryza (plant)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsSotelo-Parrilla, P. / Hari Sundar G, V. / Raju, S. / Jha, S. / Gireesh, A. / Gut, F. / Vinothkumar, K.R. / Berger, F. / Shivaprasad, P.V. / Jeyaprakash, A.A.
Funding supportEuropean Union, United Kingdom, India, 3items
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, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Apr 23, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_admin.last_update
Revision 1.3May 7, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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 H2A.2
B: Histone H2A.2
C: Histone H2B.4
D: Histone H2B.4
E: Histone H3.2
F: Histone H3.2
G: Histone H4
H: Histone H4
I: WIDOM 601
J: WIDOM 601


Theoretical massNumber of molelcules
Total (without water)204,68510
Polymers204,68510
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 4 types, 8 molecules ABCDEFGH

#1: Protein Histone H2A.2 / H2A


Mass: 13999.209 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza (plant) / Gene: OsI_025469 / Production host: Escherichia coli (E. coli) / References: UniProt: A2YMC6
#2: Protein Histone H2B.4 / H2B


Mass: 16539.408 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza (plant) / Gene: H2B.4, OsI_000388 / Production host: Escherichia coli (E. coli) / References: UniProt: A2WKP5
#3: Protein Histone H3.2 / H3


Mass: 15300.968 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza (plant) / Gene: OsI_019426, OsI_021009, OsI_021012, OsI_033964 / Production host: Escherichia coli (E. coli) / References: UniProt: A2Y533
#4: Protein Histone H4


Mass: 11436.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza (plant) / Production host: Escherichia coli (E. coli)

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain WIDOM 601


Mass: 45330.867 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain WIDOM 601


Mass: 44801.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: Rice canonical nucleosome core particle with widom 601 DNA sequence
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Oryza (plant)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140877 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310831
ELECTRON MICROSCOPYf_angle_d0.50315642
ELECTRON MICROSCOPYf_dihedral_angle_d26.7944432
ELECTRON MICROSCOPYf_chiral_restr0.0321787
ELECTRON MICROSCOPYf_plane_restr0.0041151

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