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- PDB-3j0g: Homology model of E3 protein of Venezuelan Equine Encephalitis Vi... -

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Entry
Database: PDB / ID: 3j0g
TitleHomology model of E3 protein of Venezuelan Equine Encephalitis Virus TC-83 strain fitted with a cryo-EM map
DescriptorE3 protein (E.C.3.4.21.90)
KeywordsVIRUS / alphavirus / bioweapon / VEEV
Specimen sourceVenezuelan equine encephalitis virus / virus / VEEV / ベネズエラウマ脳炎ウイルス
MethodElectron microscopy (4.8 A resolution / Single particle / Vitreous ice (cryo EM))
AuthorsZhang, R. / Hryc, C.F. / Chiu, W.
CitationEMBO J., 2011, 30, 3854-3863

EMBO J., 2011, 30, 3854-3863 StrPapers
4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus.
Rui Zhang / Corey F Hryc / Yao Cong / Xiangan Liu / Joanita Jakana / Rodion Gorchakov / Matthew L Baker / Scott C Weaver / Wah Chiu

DateDeposition: Jul 21, 2011 / Release: Aug 24, 2011 / Last modification: Jul 17, 2013

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-5275
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Assembly

Deposited unit
M: E3 protein
N: E3 protein
O: E3 protein
P: E3 protein


Theoretical massNumber of molelcules
Total (without water)25,9554
Polyers25,9554
Non-polymers00
Water0
#1
M: E3 protein
N: E3 protein
O: E3 protein
P: E3 protein
x 60


Theoretical massNumber of molelcules
Total (without water)1,557,274240
Polyers1,557,274240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
#2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
#3
M: E3 protein
N: E3 protein
O: E3 protein
P: E3 protein
x 5


  • icosahedral pentamer
  • 130 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)129,77320
Polyers129,77320
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#4
M: E3 protein
N: E3 protein
O: E3 protein
P: E3 protein
x 6


  • icosahedral 23 hexamer
  • 156 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)155,72724
Polyers155,72724
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
PAU


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

#1: Polypeptide(L)
E3 protein / Spike glycoprotein E3


Mass: 6488.640 Da / Num. of mol.: 4 / Fragment: UNP residues 276-334
Source: (natural) Venezuelan equine encephalitis virus / virus / ベネズエラウマ脳炎ウイルス
References: UniProt: P05674

Cellular component

Molecular function

Biological process

  • clathrin-dependent endocytosis of virus by host cell (GO: 0075512)
  • fusion of virus membrane with host endosome membrane (GO: 0039654)
  • virion attachment to host cell (GO: 0019062)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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Sample preparation

Assembly of specimenName: Venezuelan Equine Encephalitis Virus TC-83 Strain / Aggregation state: PARTICLE
Details: The virus contains 240 copies of E1, E2, E3 and capsid proteins
ComponentName: Venezuelan Equine Encephalitis Virus TC83 strain E3 protein that is cleaved from p62 protein
Details of the virusEmpty: NO / Enveloped: YES / Virus host category: VERTEBRATES / Virus host growth cell: Baby Hamster Kidney cells / Virus host species: Equus / Virus isolate: STRAIN / Virus type: VIRION
Buffer solutionName: TEN buffer
Sample preparationpH: 7.4
Specimen supportDetails: two of the eight grids used for imaging contained continuous carbon film underneath the samples
VitrificationInstrument: Vitrobot (FEI Inc) / Cryogen name: ETHANE / Temp: 89.34 K / Humidity: 100 % / Details: vitrification carried out in Chiu lab, Houston, TX
Method: 2 blots, each blot 2 second before plunging, offset = 0

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Electron microscopy imaging

MicroscopyMicroscope model: JEOL 3200FSC / Date: Apr 9, 2008 / Details: omega energy filter
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 / Electron dose: 18 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 100000 / Nominal defocus max: 2500 / Nominal defocus min: 400 / Cs: 4.3
Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Energy filter: Omega Filter
Specimen holderSpecimen holder model: JEM3200FSC CRYOHOLDER / Specimen holder type: Eucentric / Temperature: 96 / Tilt angle max: 0 / Tilt angle min: 0
CameraType: Gatan 4kx4k CCD Camera
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Image selectionSoftware name: CHIMERA
EM single particle entitySymmetry type: ICOSAHEDRAL
3D reconstructionMethod: projection matching / Software: EMAN / Resolution: 4.8 / Number of particles: 37000 / Nominal pixel size: 1.07
CTF correction method: CTF parameters were determined from particles within each CCD image
Details: After each iteration, the non-icosahedral parts (which included the lipids and the RNA) in the reconstruction were removed by a soft-edged mask derived from an icosahedrally organized, protein-only map that was low-pass filtered to 30 Angstroms. This map then served as the reference model for the next iteration.
Euler angles details: The structure was further refined with EMAN1 using the standard projection matching method with progressively decreasing angular step size (with a final value of 0.4 degrees).
Number of class averages: 3328
Atomic model buildingMethod: rigid-body fitting / Software name: CHIMERA
Details: The E3 homology model was not further refined against the cryo-EM density map due to its less-resolved quality
Ref space: REAL
Atomic model buildingPDB-ID: 3N40
Number of atoms included #LASTProtein: 1800 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1800

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