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

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Basic information

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 Å resolution / Particle / Single particle)
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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 21, 2011 / Release: Aug 24, 2011
RevisionDateData content typeGroupProviderType
1.0Aug 24, 2011Structure modelrepositoryInitial release
1.1Jul 17, 2013Structure modelOther

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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)25,9544
Polyers25,9544
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)1,557,264240
Polyers1,557,264240
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)129,77220
Polyers129,77220
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)155,72624
Polyers155,72624
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
#5


  • 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: 6488.601 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 experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Venezuelan Equine Encephalitis Virus TC83 strain E3 protein that is cleaved from p62 protein
Type: VIRUS
Details: The virus contains 240 copies of E1, E2, E3 and capsid proteins
Details of virusEmpty: NO / Enveloped: YES / Virus host category: VERTEBRATES / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Cricetinae / Strain: Baby Hamster Kidney cells
Buffer solutionName: TEN buffer / Details: TEN buffer / pH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: two of the eight grids used for imaging contained continuous carbon film underneath the samples
VitrificationInstrument: FEI VITROBOT MARK I / 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 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 100000 / Nominal defocus max: 2500 nm / Nominal defocus min: 400 nm / Cs: 4.3 mm
Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Specimen holderSpecimen holder model: JEOL 3200FSC CRYOHOLDER / Specimen holder type: Eucentric / Temperature: 96 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 18 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
EM imaging opticsEnergyfilter name: Omega Filter

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Processing

EM software
IDNameCategory
1UCSF ChimeraMODEL FITTING
2EMANRECONSTRUCTION
CTF correctionDetails: CTF parameters were determined from particles within each CCD image
SymmetryPoint symmetry: I
3D reconstructionMethod: projection matching / Resolution: 4.8 Å / Number of particles: 37000 / Nominal pixel size: 1.07
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.
Number of class averages: 3328 / Symmetry type: POINT
Atomic model buildingDetails: METHOD--rigid-body fitting DETAILS--The E3 homology model was not further refined against the cryo-EM density map due to its less-resolved quality
Ref protocol: RIGID BODY FIT / 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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