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- PDB-8q16: CryoEM structure of rice nucleosome containing a H4 variant chimera -

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Basic information

Entry
Database: PDB / ID: 8q16
TitleCryoEM structure of rice nucleosome containing a H4 variant chimera
Components
  • (WIDOM 601) x 2
  • Chimeric H4.V
  • Histone H2A.2
  • Histone H2B.4
  • Histone H3.2
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 H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A ...: / 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 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: Gandhivel, V.H.S. / Sotelo-Parrilla, P. / Raju, S. / Jha, S. / Gireesh, A. / Harshith, C.Y. / Gut, F. / Vinothkumar, K.R. / Berger, F. / Jeyaprakash, A.A. / Shivaprasad, P.V.
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

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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: Chimeric H4.V
H: Chimeric H4.V
I: WIDOM 601
J: WIDOM 601


Theoretical massNumber of molelcules
Total (without water)205,51210
Polymers205,51210
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 Chimeric H4.V


Mass: 11541.646 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: 45604.047 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain WIDOM 601


Mass: 45145.754 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 nucleosome core particle containing a histone H4 variant chimera with Widom 601 DNA
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: 148217 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00412583
ELECTRON MICROSCOPYf_angle_d0.53618252
ELECTRON MICROSCOPYf_dihedral_angle_d26.9525168
ELECTRON MICROSCOPYf_chiral_restr0.0332087
ELECTRON MICROSCOPYf_plane_restr0.0041280

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