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- EMDB-5276: 4.4 Angstrom Cryo-EM Structure of an Enveloped Alphavirus Venezue... -

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Basic information

Entry
Database: EMDB / ID: EMD-5276
Title4.4 Angstrom Cryo-EM Structure of an Enveloped Alphavirus Venezuelan Equine Encephalitis Virus
Map dataThis is a non-icosahedrally averaged map of Venezuelan Equine Encephalitis Virus from the 4 unique sets of E1-E2-E3-CP molecules within one asymmetric unit of the original 3D density map.
Sample
  • Sample: Venezuelan Equine Encephalitis Virus TC-83 Strain
  • Virus: Venezuelan equine encephalitis virus
Keywordsalphavirus / bioweapon / cryoEM / modeling / VEEV
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / symbiont-mediated suppression of host gene expression / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / symbiont-mediated suppression of host gene expression / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / proteolysis / RNA binding / membrane
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesVenezuelan equine encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsZhang R / Hryc CF / Cong Y / Liu X / Jakana J / Gorchakov R / Baker ML / Weaver SC / Chiu W
CitationJournal: EMBO J / Year: 2011
Title: 4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus.
Authors: Rui Zhang / Corey F Hryc / Yao Cong / Xiangan Liu / Joanita Jakana / Rodion Gorchakov / Matthew L Baker / Scott C Weaver / Wah Chiu /
Abstract: Venezuelan equine encephalitis virus (VEEV), a member of the membrane-containing Alphavirus genus, is a human and equine pathogen, and has been developed as a biological weapon. Using electron cryo- ...Venezuelan equine encephalitis virus (VEEV), a member of the membrane-containing Alphavirus genus, is a human and equine pathogen, and has been developed as a biological weapon. Using electron cryo-microscopy (cryo-EM), we determined the structure of an attenuated vaccine strain, TC-83, of VEEV to 4.4 Å resolution. Our density map clearly resolves regions (including E1, E2 transmembrane helices and cytoplasmic tails) that were missing in the crystal structures of domains of alphavirus subunits. These new features are implicated in the fusion, assembly and budding processes of alphaviruses. Furthermore, our map reveals the unexpected E3 protein, which is cleaved and generally thought to be absent in the mature VEEV. Our structural results suggest a mechanism for the initial stage of nucleocapsid core formation, and shed light on the virulence attenuation, host recognition and neutralizing activities of VEEV and other alphavirus pathogens.
History
DepositionApr 15, 2011-
Header (metadata) releaseApr 19, 2011-
Map releaseAug 16, 2011-
UpdateSep 19, 2012-
Current statusSep 19, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j0c
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j0c
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5276_1.png

Downloads & links

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Map

FileDownload / File: emd_5276.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a non-icosahedrally averaged map of Venezuelan Equine Encephalitis Virus from the 4 unique sets of E1-E2-E3-CP molecules within one asymmetric unit of the original 3D density map.
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 6.0 / Movie #1: 6
Minimum - Maximum-13.587567330000001 - 32.44748688
Average (Standard dev.)-0.00455169 (±0.93261677)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin32-47-297
Dimensions192192192
Spacing192192192
CellA=B=C: 205.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z205.440205.440205.440
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-4732-297
NC/NR/NS192192192
D min/max/mean-13.58832.447-0.005

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Supplemental data

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Sample components

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Entire : Venezuelan Equine Encephalitis Virus TC-83 Strain

EntireName: Venezuelan Equine Encephalitis Virus TC-83 Strain
Components
  • Sample: Venezuelan Equine Encephalitis Virus TC-83 Strain
  • Virus: Venezuelan equine encephalitis virus

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Supramolecule #1000: Venezuelan Equine Encephalitis Virus TC-83 Strain

SupramoleculeName: Venezuelan Equine Encephalitis Virus TC-83 Strain / type: sample / ID: 1000
Details: The viruses were purified from infected Baby hamster kidney (BHK) cells
Oligomeric state: E1-E2-E3-CP complex / Number unique components: 4
Molecular weightTheoretical: 52 MDa

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Supramolecule #1: Venezuelan equine encephalitis virus

SupramoleculeName: Venezuelan equine encephalitis virus / type: virus / ID: 1 / Name.synonym: VEEV / NCBI-ID: 11036 / Sci species name: Venezuelan equine encephalitis virus / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: VEEV
Host (natural)Organism: Equus caballus (horse) / synonym: VERTEBRATES
Molecular weightTheoretical: 52 MDa
Virus shellShell ID: 1 / Diameter: 700 Å / T number (triangulation number): 4

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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
GridDetails: 400 mesh Quantifoil R 1.2/1.3 copper grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: 2 blots, each blot 2 seconds before plunging

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Electron microscopy

MicroscopeJEOL 3200FSC
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 4.3 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 100000
Specialist opticsEnergy filter - Name: Omega Filter
Sample stageSpecimen holder: Eucentric / Specimen holder model: JEOL 3200FSC CRYOHOLDER
TemperatureAverage: 96 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
DateApr 9, 2008
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Number real images: 4000 / Average electron dose: 18 e/Å2 / Camera length: 200 / Details: 4kx4k CCD Image

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Image processing

CTF correctionDetails: Each frame
Final two d classificationNumber classes: 1000
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN
Details: This is a non-icosahedrally averaged map of Venezuelan Equine Encephalitis Virus from the 4 unique sets of E1-E2-E3-CP molecules within one asymmetric unit of the original 3D density map
Number images used: 37000
DetailsThe virus particles were automatically boxed out using ethan, among which around 10,000 particles contained continuous carbon film.

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Atomic model buiding 1

Initial modelPDB ID:

3n40

DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-3j0c:
Models of E1, E2 and CP of Venezuelan Equine Encephalitis Virus TC-83 strain restrained by a near atomic resolution cryo-EM map

PDB-3j0g:
Homology model of E3 protein of Venezuelan Equine Encephalitis Virus TC-83 strain fitted with a cryo-EM map

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