[English] 日本語
Yorodumi
- PDB-7lv8: Structure of the Marseillevirus nucleosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lv8
TitleStructure of the Marseillevirus nucleosome
Components
  • (DNA (123-MER)) x 2
  • (Histone doublet Beta-Alpha ...) x 2
  • (Histone doublet Delta-Gamma ...) x 2
KeywordsSTRUCTURAL PROTEIN/DNA / STRUCTURAL PROTEIN / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding
Similarity search - Function
Histone H2A / Histone 2A / 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/H2A fusion protein / Histone H3 / Histone H2B/H2A fusion protein
Similarity search - Component
Biological speciesMarseillevirus marseillevirus
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsValencia-Sanchez, M.I. / Abini-Agbomson, S. / Armache, K.-J.
Funding support United States, 2items
OrganizationGrant numberCountry
David and Lucile Packard Foundationna United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM115882-03 United States
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: The structure of a virus-encoded nucleosome.
Authors: Marco Igor Valencia-Sánchez / Stephen Abini-Agbomson / Miao Wang / Rachel Lee / Nikita Vasilyev / Jenny Zhang / Pablo De Ioannes / Bernard La Scola / Paul Talbert / Steve Henikoff / Evgeny ...Authors: Marco Igor Valencia-Sánchez / Stephen Abini-Agbomson / Miao Wang / Rachel Lee / Nikita Vasilyev / Jenny Zhang / Pablo De Ioannes / Bernard La Scola / Paul Talbert / Steve Henikoff / Evgeny Nudler / Albert Erives / Karim-Jean Armache /
Abstract: Certain large DNA viruses, including those in the Marseilleviridae family, encode histones. Here we show that fused histone pairs Hβ-Hα and Hδ-Hγ from Marseillevirus are structurally analogous to ...Certain large DNA viruses, including those in the Marseilleviridae family, encode histones. Here we show that fused histone pairs Hβ-Hα and Hδ-Hγ from Marseillevirus are structurally analogous to the eukaryotic histone pairs H2B-H2A and H4-H3. These viral histones form 'forced' heterodimers, and a heterotetramer of four such heterodimers assembles DNA to form structures virtually identical to canonical eukaryotic nucleosomes.
History
DepositionFeb 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 26, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-23529
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Histone doublet Delta-Gamma (Delta)
A: Histone doublet Delta-Gamma (Gamma)
D: Histone doublet Beta-Alpha (Beta)
C: Histone doublet Beta-Alpha (Alpha)
F: Histone doublet Delta-Gamma (Delta)
E: Histone doublet Delta-Gamma (Gamma)
H: Histone doublet Beta-Alpha (Beta)
G: Histone doublet Beta-Alpha (Alpha)
I: DNA (123-MER)
J: DNA (123-MER)


Theoretical massNumber of molelcules
Total (without water)176,95110
Polymers176,95110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Histone doublet Delta-Gamma ... , 2 types, 4 molecules BFAE

#1: Protein Histone doublet Delta-Gamma (Delta) / Histone H3


Mass: 10462.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marseillevirus marseillevirus / Gene: MAR_ORF413 / Production host: Escherichia coli (E. coli) / References: UniProt: D2XB48
#2: Protein Histone doublet Delta-Gamma (Gamma) / Histone H3


Mass: 11767.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marseillevirus marseillevirus / Gene: MAR_ORF413 / Production host: Escherichia coli (E. coli) / References: UniProt: D2XB48

-
Histone doublet Beta-Alpha ... , 2 types, 4 molecules DHCG

#3: Protein Histone doublet Beta-Alpha (Beta) / Histone H2B/H2A fusion protein


Mass: 11228.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marseillevirus marseillevirus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2R3ZQX0
#4: Protein Histone doublet Beta-Alpha (Alpha) / Histone H2B/H2A fusion protein


Mass: 17675.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marseillevirus marseillevirus / Gene: MAR_ORF414 / Production host: Escherichia coli (E. coli) / References: UniProt: D2XB49

-
DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (123-MER)


Mass: 37530.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (123-MER)


Mass: 37152.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Structure of the Marseillevirus nucleosome / Type: COMPLEX / Details: virus-encoded histone doublets Marseillevirus / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21synthetic construct (others)32630
11Marseillevirus marseillevirus694581
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHepesHepes1
21 mMEDTAEDTA1
32 mMDTTDTT1
SpecimenConc.: 3.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 297 K

-
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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 65 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4503
EM imaging opticsEnergyfilter slit width: 20 eV

-
Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
EM software
IDNameVersionCategory
2Leginonimage acquisition
4CTFFINDcryoSPARCCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10PHENIXmodel refinement
11cryoSPARC2.15initial Euler assignment
12cryoSPARC2.15final Euler assignment
13cryoSPARCclassification
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3017414
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146506 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
11KX5

1kx5

1KX51
23LZ0

3lz0

I3LZ02
33LZ0

3lz0

J3LZ02
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311353
ELECTRON MICROSCOPYf_angle_d0.62216345
ELECTRON MICROSCOPYf_dihedral_angle_d30.6053226
ELECTRON MICROSCOPYf_chiral_restr0.0371893
ELECTRON MICROSCOPYf_plane_restr0.0041220

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more