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- EMDB-5160: Atomic CryoEM Structure of a Non-Enveloped Virus Reveals How its ... -

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Basic information

Entry
Database: EMDB / ID: EMD-5160
TitleAtomic CryoEM Structure of a Non-Enveloped Virus Reveals How its Membrane Protein is Primed for Cell Entry
Map dataAquareovirus filtered to 3.2A
Sample
  • Sample: Aquareovirus
  • Virus: Aquareovirus
KeywordsAtomic CryoEM Non-enveloped Virus Membrane penetration Protein Autocleavage
Function / homology
Function and homology information


symbiont entry into host cell via permeabilization of inner membrane / permeabilization of host organelle membrane involved in viral entry into host cell / viral inner capsid / host cell surface binding / viral outer capsid / 7-methylguanosine mRNA capping / viral capsid / mRNA guanylyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity ...symbiont entry into host cell via permeabilization of inner membrane / permeabilization of host organelle membrane involved in viral entry into host cell / viral inner capsid / host cell surface binding / viral outer capsid / 7-methylguanosine mRNA capping / viral capsid / mRNA guanylyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / hydrolase activity / RNA helicase / GTP binding / ATP binding / metal ion binding
Similarity search - Function
Outer capsid protein Mu1/VP4 / Mu1 membrane penetration protein, domain IV / Mu1 membrane penetration protein, domain II / Mu1/VP4 superfamily / Mu1 membrane penetration protein, domain III / 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 ...Outer capsid protein Mu1/VP4 / Mu1 membrane penetration protein, domain IV / Mu1 membrane penetration protein, domain II / Mu1/VP4 superfamily / Mu1 membrane penetration protein, domain III / 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
Core protein VP6 / Putative outer capsid VP4 / RNA helicase / VP1
Similarity search - Component
Biological speciesAquareovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhang X / Jin L / Fang Q / Hui WH / Zhou ZH
CitationJournal: Cell / Year: 2010
Title: 3.3 A cryo-EM structure of a nonenveloped virus reveals a priming mechanism for cell entry.
Authors: Xing Zhang / Lei Jin / Qin Fang / Wong H Hui / Z Hong Zhou /
Abstract: To achieve cell entry, many nonenveloped viruses must transform from a dormant to a primed state. In contrast to the membrane fusion mechanism of enveloped viruses (e.g., influenza virus), this ...To achieve cell entry, many nonenveloped viruses must transform from a dormant to a primed state. In contrast to the membrane fusion mechanism of enveloped viruses (e.g., influenza virus), this membrane penetration mechanism is poorly understood. Here, using single-particle cryo-electron microscopy, we report a 3.3 A structure of the primed, infectious subvirion particle of aquareovirus. The density map reveals side-chain densities of all types of amino acids (except glycine), enabling construction of a full-atom model of the viral particle. Our structure and biochemical results show that priming involves autocleavage of the membrane penetration protein and suggest that Lys84 and Glu76 may facilitate this autocleavage in a nucleophilic attack. We observe a myristoyl group, covalently linked to the N terminus of the penetration protein and embedded in a hydrophobic pocket. These results suggest a well-orchestrated process of nonenveloped virus entry involving autocleavage of the penetration protein prior to exposure of its membrane-insertion finger.
History
DepositionJan 18, 2010-
Header (metadata) releaseMay 3, 2010-
Map releaseMay 3, 2010-
UpdateDec 26, 2012-
Current statusDec 26, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3iyl
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3iyl
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5160_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5160.map.gz / Format: CCP4 / Size: 1.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAquareovirus filtered to 3.2A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 740 pix.
= 814. Å		1.1 Å/pix.
x 740 pix.
= 814. Å		1.1 Å/pix.
x 740 pix.
= 814. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.05 / Movie #1: 0.04
Minimum - Maximum-0.19343019 - 0.30496365
Average (Standard dev.)-0.00054387 (±0.02425474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-370-370-370
Dimensions740740740
Spacing740740740
CellA=B=C: 814.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z740740740
origin x/y/z0.0000.0000.000
length x/y/z814.000814.000814.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-370-370-370
NC/NR/NS740740740
D min/max/mean-0.1930.305-0.001

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Supplemental data

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Segmentation: averaged VP5 protein at 3.2a.

Annotationaveraged VP5 protein at 3.2a.
Fileemd_5160_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Aquareovirus

EntireName: Aquareovirus
Components
  • Sample: Aquareovirus
  • Virus: Aquareovirus

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Supramolecule #1000: Aquareovirus

SupramoleculeName: Aquareovirus / type: sample / ID: 1000 / Details: The sample was monodisperse / Number unique components: 4
Molecular weightExperimental: 72 MDa / Theoretical: 72 MDa

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Supramolecule #1: Aquareovirus

SupramoleculeName: Aquareovirus / type: virus / ID: 1 / Name.synonym: GCRV / NCBI-ID: 10979 / Sci species name: Aquareovirus / Database: NCBI / Virus type: OTHER / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: GCRV
Host (natural)synonym: VERTEBRATES
Molecular weightExperimental: 72 MDa / Theoretical: 72 MDa
Virus shellShell ID: 1 / Name: ISVP / Diameter: 800 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

BufferpH: 7.5 / Details: 10mM PBS Buffer
GridDetails: 400 mesh quantifoil 1.2/1.3
VitrificationCryogen name: METHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: OTHER / Details: Vitrification instrument: FEI Vitrobot / Method: Blot for 7-9 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 90 K / Average: 90 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 250,000 times magnification
DateMar 1, 2009
Image recordingCategory: CCD / Film or detector model: KODAK SO-163 FILM / Digitization - Sampling interval: 6.35 µm / Number real images: 700 / Average electron dose: 25 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 57700 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 59000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Frealign IMIRS / Number images used: 18464
Final angle assignmentDetails: Frealign IMIRS

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