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- EMDB-1653: Aquareovirus capsid proteins. -

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Basic information

Entry
Database: EMDB / ID: EMD-1653
TitleAquareovirus capsid proteins.
Map dataVP1 protein
Sample
  • Sample: Grass carp reovirus
  • Virus: Grass carp reovirus
Keywordsaquareovirus / capsid proteins / grass carp reovirus
Function / homology
Function and homology information


host cell surface binding / viral inner capsid / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / 7-methylguanosine mRNA capping / viral capsid / mRNA guanylyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity ...host cell surface binding / viral inner capsid / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / 7-methylguanosine mRNA capping / viral capsid / mRNA guanylyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / RNA helicase / hydrolase activity / GTP binding / ATP binding / metal ion binding
Similarity search - Function
Outer capsid protein VP7 / Outer capsid protein VP7 / Mu1 membrane penetration protein, domain III / Outer capsid protein Mu1/VP4 / Mu1 membrane penetration protein, domain IV / Mu1 membrane penetration protein, domain II / Mu1/VP4 superfamily / Reovirus major virion structural protein Mu-1/Mu-1C (M2) / Sigma1/sigma2, reoviral / Reoviral Sigma1/Sigma2 family ...Outer capsid protein VP7 / Outer capsid protein VP7 / Mu1 membrane penetration protein, domain III / Outer capsid protein Mu1/VP4 / Mu1 membrane penetration protein, domain IV / Mu1 membrane penetration protein, domain II / Mu1/VP4 superfamily / Reovirus major virion structural protein Mu-1/Mu-1C (M2) / Sigma1/sigma2, reoviral / Reoviral Sigma1/Sigma2 family / Reovirus core-spike lambda-2 / Reovirus core-spike protein lambda-2 (L2), C-terminal / Inner capsid protein lambda-1/ VP3 / C2H2-type zinc finger / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Outer capsid VP7 / Core protein VP6 / Putative outer capsid VP4 / RNA helicase / VP1
Similarity search - Component
Biological speciesGrass carp reovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsCheng L / Zhu J / Hui WH / Zhang X / Honig B / Fang Q / Zhou ZH
CitationJournal: J Mol Biol / Year: 2010
Title: Backbone model of an aquareovirus virion by cryo-electron microscopy and bioinformatics.
Authors: Lingpeng Cheng / Jiang Zhu / Wong Hoi Hui / Xiaokang Zhang / Barry Honig / Qin Fang / Z Hong Zhou /
Abstract: Grass carp reovirus (GCRV) is a member of the aquareovirus genus in the Reoviridae family and has a capsid with two shells-a transcription-competent core surrounded by a coat. We report a near-atomic- ...Grass carp reovirus (GCRV) is a member of the aquareovirus genus in the Reoviridae family and has a capsid with two shells-a transcription-competent core surrounded by a coat. We report a near-atomic-resolution reconstruction of the GCRV virion by cryo-electron microscopy and single-particle reconstruction. A backbone model of the GCRV virion, including seven conformers of the five capsid proteins making up the 1500 molecules in both the core and the coat, was derived using cryo-electron microscopy density-map-constrained homology modeling and refinement. Our structure clearly showed that the amino-terminal segment of core protein VP3B forms an approximately 120-A-long alpha-helix-rich extension bridging across the icosahedral 2-fold-symmetry-related molecular interface. The presence of this unique structure across this interface and the lack of an external cementing molecule at this location in GCRV suggest a stabilizing role of this extended amino-terminal density. Moreover, part of this amino-terminal extension becomes invisible in the reconstruction of transcription-competent core particles, suggesting its involvement in endogenous viral RNA transcription. Our structure of the VP1 turret represents its open state, and comparison with its related structures at the closed state suggests hinge-like domain movements associated with the mRNA-capping machinery. Overall, this first backbone model of an aquareovirus virion provides a wealth of structural information for understanding the structural basis of GCRV assembly and transcription.
History
DepositionSep 25, 2009-
Header (metadata) releaseAug 19, 2011-
Map releaseAug 19, 2011-
UpdateSep 8, 2011-
Current statusSep 8, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

em-1653.png

Downloads & links

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Map

FileDownload / File: emd_1653.map.gz / Format: CCP4 / Size: 1.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVP1 protein
Voxel sizeX=Y=Z: 0.9716 Å
Density
Contour LevelBy AUTHOR: 1.4 / Movie #1: 1.4
Minimum - Maximum-8.590540000000001 - 6.45957
Average (Standard dev.)0.0260624 (±0.721239)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-465-4650
Dimensions929929465
Spacing929929465
CellA: 901.645 Å / B: 901.645 Å / C: 450.822 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.971600215517240.971600215517240.97159913793103
M x/y/z928928464
origin x/y/z0.0000.0000.000
length x/y/z901.645901.645450.822
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-465-4650
NC/NR/NS929929465
D min/max/mean-8.5916.4600.026

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Supplemental data

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Sample components

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Entire : Grass carp reovirus

EntireName: Grass carp reovirus
Components
  • Sample: Grass carp reovirus
  • Virus: Grass carp reovirus

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Supramolecule #1000: Grass carp reovirus

SupramoleculeName: Grass carp reovirus / type: sample / ID: 1000 / Details: The sample is Grass carp reovirus virion / Number unique components: 1

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Supramolecule #1: Grass carp reovirus

SupramoleculeName: Grass carp reovirus / type: virus / ID: 1 / Name.synonym: GCRV / NCBI-ID: 128987 / Sci species name: Grass carp reovirus / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Syn species name: GCRV
Host (natural)synonym: VERTEBRATES
Virus shellShell ID: 1 / Diameter: 880 Å / T number (triangulation number): 13

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferDetails: PBS
VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.3 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 93000
Sample stageSpecimen holder: FEI / Specimen holder model: PHILIPS ROTATION HOLDER
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Number real images: 4000 / Average electron dose: 20 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each micrograph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: OTHER / Software - Name: IMIRS / Number images used: 15000

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