[English] 日本語
Yorodumi
- EMDB-6969: Structure of RNA polymerase complex and genome within a dsRNA vir... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 6969
TitleStructure of RNA polymerase complex and genome within a dsRNA virus provides insights into the mechanisms of transcription and assembly
Map dataIcosahedral capsid of aquareovirus
SampleGrass carp reovirus:
virus / Outer capsid VP7 / N-terminus of outer capsid protein VP5 / C-terminus of outer capsid protein VP5 / Core protein VP6 / VP1 / VP3 / ligand
Function / homologyMu1 membrane penetration protein, subdomain 3 / Reovirus core-spike protein lambda-2 (L2) / Reoviral Sigma1/Sigma2 family / Mu1/VP4 superfamily / Outer capsid protein VP7 / Mu1 membrane penetration protein, subdomain 2 / Immunoglobulin-like fold / Zinc finger C2H2-type / Reovirus core-spike lambda-2 / Outer capsid protein Mu1/VP4 ...Mu1 membrane penetration protein, subdomain 3 / Reovirus core-spike protein lambda-2 (L2) / Reoviral Sigma1/Sigma2 family / Mu1/VP4 superfamily / Outer capsid protein VP7 / Mu1 membrane penetration protein, subdomain 2 / Immunoglobulin-like fold / Zinc finger C2H2-type / Reovirus core-spike lambda-2 / Outer capsid protein Mu1/VP4 / Sigma1/sigma2, reoviral / Outer capsid protein VP7 / Zinc finger C2H2 type domain signature. / Zinc finger C2H2 type domain profile. / Reovirus major virion structural protein Mu-1/Mu-1C (M2) / mRNA guanylyltransferase activity / host cell surface binding / viral outer capsid / mRNA (guanine-N7-)-methyltransferase activity / viral capsid / nucleic acid binding / viral entry into host cell / pathogenesis / ATP binding / Outer capsid VP7 / Core protein VP6 / Putative outer capsid VP4 / VP3 / VP1
Function and homology information
SourceGrass carp reovirus
Methodsingle particle reconstruction / cryo EM / 3.3 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 ReportPDB-ID: 5zvt

SummaryFull reportAbout validation report
DateDeposition: May 12, 2018 / Header (metadata) release: Jul 4, 2018 / Map release: Jul 4, 2018 / Last update: Jul 25, 2018

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 9
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 9
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5zvt
  • Surface level: 9
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5zvt
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_6969.map.gz (map file in CCP4 format, 2916001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
900 pix
0.93 Å/pix.
= 838.8 Å
900 pix
0.93 Å/pix.
= 838.8 Å
900 pix
0.93 Å/pix.
= 838.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density
Contour Level:9.0 (by author), 9 (movie #1):
Minimum - Maximum-88.945359999999994 - 134.412659999999988
Average (Standard dev.)0.6796208 (8.760672)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions900900900
Origin-450.-450.-450.
Limit449.449.449.
Spacing900900900
CellA=B=C: 838.8 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9320.9320.932
M x/y/z900900900
origin x/y/z0.0000.0000.000
length x/y/z838.800838.800838.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-450-450-450
NC/NR/NS900900900
D min/max/mean-88.945134.4130.680

-
Supplemental data

-
Mask #1

Fileemd_6969_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

-
Sample components

+
Entire Grass carp reovirus

EntireName: Grass carp reovirus / Number of components: 8

+
Component #1: virus, Grass carp reovirus

VirusName: Grass carp reovirus / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Grass carp reovirus
Source (engineered)Expression System: Ctenopharyngodon idella (grass carp)

+
Component #2: protein, Outer capsid VP7

ProteinName: Outer capsid VP7 / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 29.844648 kDa
SourceSpecies: Grass carp reovirus
Source (engineered)Expression System: Ctenopharyngodon idella (grass carp)

+
Component #3: protein, N-terminus of outer capsid protein VP5

ProteinName: N-terminus of outer capsid protein VP5 / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 4.302686 kDa
SourceSpecies: Grass carp reovirus
Source (engineered)Expression System: Ctenopharyngodon idella (grass carp)

+
Component #4: protein, C-terminus of outer capsid protein VP5

ProteinName: C-terminus of outer capsid protein VP5 / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 64.362086 kDa
SourceSpecies: Grass carp reovirus
Source (engineered)Expression System: Ctenopharyngodon idella (grass carp)

+
Component #5: protein, Core protein VP6

ProteinName: Core protein VP6 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 44.606535 kDa
SourceSpecies: Grass carp reovirus
Source (engineered)Expression System: Ctenopharyngodon idella (grass carp)

+
Component #6: protein, VP1

ProteinName: VP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 141.512156 kDa
SourceSpecies: Grass carp reovirus
Source (engineered)Expression System: Ctenopharyngodon idella (grass carp)

+
Component #7: protein, VP3

ProteinName: VP3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 132.203312 kDa
SourceSpecies: Grass carp reovirus
Source (engineered)Expression System: Ctenopharyngodon idella (grass carp)

+
Component #8: ligand, MYRISTIC ACID

LigandName: MYRISTIC ACID / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 0.228371 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 25 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 41000
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
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