[English] 日本語
Yorodumi
- PDB-5zvs: Structure of RNA polymerase complex and genome within a dsRNA vir... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5zvs
TitleStructure of RNA polymerase complex and genome within a dsRNA virus provides insights into the mechanisms of transcription and assembly
Components
  • Putative core protein NTPase/VP5
  • VP2
  • VP3
KeywordsVIRAL PROTEIN / icosahedral capsid / symmetry-mismatch / genome / RNA-dependent RNA polymerase
Function / homologyC2H2-type zinc finger / Reovirus RNA-dependent RNA polymerase lambda 3 / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Reovirus RNA-dependent RNA polymerase lambda 3 / Reovirus minor core protein Mu-2 / Zinc finger C2H2-type / Reovirus minor core protein, Mu-2 / RNA-directed RNA polymerase, reovirus ...C2H2-type zinc finger / Reovirus RNA-dependent RNA polymerase lambda 3 / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Reovirus RNA-dependent RNA polymerase lambda 3 / Reovirus minor core protein Mu-2 / Zinc finger C2H2-type / Reovirus minor core protein, Mu-2 / RNA-directed RNA polymerase, reovirus / viral genome replication / viral capsid / nucleic acid binding / viral nucleocapsid / RNA-directed 5'-3' RNA polymerase activity / structural molecule activity / RNA binding / Putative core protein NTPase/VP5 / VP3 / VP2
Function and homology information
Specimen sourceGrass carp reovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsLiu, H. / Fang, Q. / Cheng, L.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure of RNA polymerase complex and genome within a dsRNA virus provides insights into the mechanisms of transcription and assembly.
Authors: Xurong Wang / Fuxian Zhang / Rui Su / Xiaowu Li / Wenyuan Chen / Qingxiu Chen / Tao Yang / Jiawei Wang / Hongrong Liu / Qin Fang / Lingpeng Cheng
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 12, 2018 / Release: Jul 4, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 4, 2018Structure modelrepositoryInitial release
1.1Jul 25, 2018Structure modelData collection / Database referencescitation_citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-6968
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-6968
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VP3
B: VP3
D: VP3
C: VP3
E: VP3
F: VP3
G: VP3
H: VP3
I: VP3
J: VP3
2: VP2
4: Putative core protein NTPase/VP5


Theoretical massNumber of molelcules
Total (without water)1,544,10012
Polyers1,544,10012
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)91820
ΔGint (kcal/M)-393
Surface area (Å2)434030

-
Components

#1: Protein/peptide
VP3


Mass: 132203.312 Da / Num. of mol.: 10 / Source: (gene. exp.) Grass carp reovirus / Production host: Ctenopharyngodon idella (grass carp) / References: UniProt: Q9E3V8
#2: Protein/peptide VP2


Mass: 141685.438 Da / Num. of mol.: 1 / Source: (gene. exp.) Grass carp reovirus / Production host: Ctenopharyngodon idella (grass carp) / References: UniProt: Q9E3V9
#3: Protein/peptide Putative core protein NTPase/VP5 / cofactor protein of RNA-dependent RNA polymerase


Mass: 80381.516 Da / Num. of mol.: 1 / Source: (gene. exp.) Grass carp reovirus / Production host: Ctenopharyngodon idella (grass carp) / References: UniProt: Q8JU68

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Grass carp reovirus / Type: VIRUS / Entity ID: 1,2,3 / Source: RECOMBINANT
Source (natural)Organism: Grass carp reovirus
Source (recombinant)Organism: Ctenopharyngodon idella (grass carp)
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: STRAIN / Virus type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 / C2 aperture diameter: 70
Image recordingElectron dose: 25 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 41000 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008101802
ELECTRON MICROSCOPYf_angle_d0.878139478
ELECTRON MICROSCOPYf_dihedral_angle_d15.00961378
ELECTRON MICROSCOPYf_chiral_restr0.05416235
ELECTRON MICROSCOPYf_plane_restr0.00918125

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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