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- EMDB-6968: Structure of RNA polymerase complex and genome within a dsRNA vir... -

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Basic information

Entry
Database: EMDB / ID: 6968
TitleStructure of RNA polymerase complex and genome within a dsRNA virus provides insights into the mechanisms of transcription and assembly
Map dataSymmetry-mismatch structure of aquareovirus
SampleGrass carp reovirus:
virus / VP3 / VP2 / Putative core protein NTPase/VP5
Function / homologyReovirus RNA-dependent RNA polymerase lambda 3 / Reovirus minor core protein Mu-2 / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / RNA-directed RNA polymerase, reovirus / Reovirus minor core protein, Mu-2 / Reovirus RNA-dependent RNA polymerase lambda 3 / Zinc finger C2H2-type / viral genome replication ...Reovirus RNA-dependent RNA polymerase lambda 3 / Reovirus minor core protein Mu-2 / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / RNA-directed RNA polymerase, reovirus / Reovirus minor core protein, Mu-2 / Reovirus RNA-dependent RNA polymerase lambda 3 / Zinc finger C2H2-type / viral genome replication / viral capsid / nucleic acid binding / RNA-directed 5'-3' RNA polymerase activity / viral nucleocapsid / structural molecule activity / RNA binding / Putative core protein NTPase/VP5 / VP3 / VP2
Function and homology information
SourceGrass carp reovirus
Methodsingle 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 ReportPDB-ID: 5zvs

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

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5zvs
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5zvs
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6968.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:8.0 (by author), 8 (movie #1):
Minimum - Maximum-26.853725000000001 - 54.858490000000003
Average (Standard dev.)0.73939174 (4.089046)
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-26.85454.8580.739

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Supplemental data

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Sample components

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Entire Grass carp reovirus

EntireName: Grass carp reovirus / Number of components: 4

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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)

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Component #2: protein, VP3

ProteinName: VP3 / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 132.203312 kDa
SourceSpecies: Grass carp reovirus
Source (engineered)Expression System: Ctenopharyngodon idella (grass carp)

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Component #3: protein, VP2

ProteinName: VP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 141.685438 kDa
SourceSpecies: Grass carp reovirus
Source (engineered)Expression System: Ctenopharyngodon idella (grass carp)

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Component #4: protein, Putative core protein NTPase/VP5

ProteinName: Putative core protein NTPase/VP5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 80.381516 kDa
SourceSpecies: Grass carp reovirus
Source (engineered)Expression System: Ctenopharyngodon idella (grass carp)

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Experimental details

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Sample preparation

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

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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
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 41000
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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