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- PDB-3j0c: Models of E1, E2 and CP of Venezuelan Equine Encephalitis Virus T... -

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Basic information

Entry
Database: PDB / ID: 3j0c
TitleModels of E1, E2 and CP of Venezuelan Equine Encephalitis Virus TC-83 strain restrained by a near atomic resolution cryo-EM map
Components
  • Capsid proteinCapsid
  • E1 envelope glycoprotein
  • E2 envelope glycoprotein
KeywordsVIRUS / alphavirus / bioweapon
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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsZhang, R. / Hryc, C.F. / Cong, Y. / Liu, X. / Jakana, J. / Gorchakov, R. / Baker, M.L. / Weaver, S.C. / 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
DepositionJun 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_imaging_optics / em_software
Item: _em_imaging_optics.energyfilter_name / _em_software.image_processing_id

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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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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  • Simplified surface model + fitted atomic model
  • EMDB-5276
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  • Superimposition on EM map
  • EMDB-5276
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: E1 envelope glycoprotein
B: E2 envelope glycoprotein
C: Capsid protein
D: E1 envelope glycoprotein
E: E2 envelope glycoprotein
F: Capsid protein
G: E1 envelope glycoprotein
H: E2 envelope glycoprotein
I: Capsid protein
J: E1 envelope glycoprotein
K: E2 envelope glycoprotein
L: Capsid protein


Theoretical massNumber of molelcules
Total (without water)453,04712
Polymers453,04712
Non-polymers00
Water0
1
A: E1 envelope glycoprotein
B: E2 envelope glycoprotein
C: Capsid protein
D: E1 envelope glycoprotein
E: E2 envelope glycoprotein
F: Capsid protein
G: E1 envelope glycoprotein
H: E2 envelope glycoprotein
I: Capsid protein
J: E1 envelope glycoprotein
K: E2 envelope glycoprotein
L: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)27,182,796720
Polymers27,182,796720
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
A: E1 envelope glycoprotein
B: E2 envelope glycoprotein
C: Capsid protein
D: E1 envelope glycoprotein
E: E2 envelope glycoprotein
F: Capsid protein
G: E1 envelope glycoprotein
H: E2 envelope glycoprotein
I: Capsid protein
J: E1 envelope glycoprotein
K: E2 envelope glycoprotein
L: Capsid protein
x 5


  • icosahedral pentamer
  • 2.27 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)2,265,23360
Polymers2,265,23360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: E1 envelope glycoprotein
B: E2 envelope glycoprotein
C: Capsid protein
D: E1 envelope glycoprotein
E: E2 envelope glycoprotein
F: Capsid protein
G: E1 envelope glycoprotein
H: E2 envelope glycoprotein
I: Capsid protein
J: E1 envelope glycoprotein
K: E2 envelope glycoprotein
L: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 2.72 MDa, 72 polymers
Theoretical massNumber of molelcules
Total (without water)2,718,28072
Polymers2,718,28072
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
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
E1 envelope glycoprotein / Spike glycoprotein E1


Mass: 47952.066 Da / Num. of mol.: 4 / Fragment: full length (UNP residues 813-1254) / Source method: isolated from a natural source
Details: purified from infected Baby hamster kidney (BHK) cells
Source: (natural) Venezuelan equine encephalitis virus / Strain: TC-83 / References: UniProt: P05674
#2: Protein
E2 envelope glycoprotein / Spike glycoprotein E2


Mass: 47113.746 Da / Num. of mol.: 4 / Fragment: full length (UNP residues 335-757) / Source method: isolated from a natural source
Details: purified from infected Baby hamster kidney (BHK) cells
Source: (natural) Venezuelan equine encephalitis virus / Strain: TC-83 / References: UniProt: P05674
#3: Protein
Capsid protein / Capsid / Coat protein / C


Mass: 18195.840 Da / Num. of mol.: 4 / Fragment: C-terminal protease domain (UNP residues 114-275) / Source method: isolated from a natural source
Details: purified from infected Baby hamster kidney (BHK) cells
Source: (natural) Venezuelan equine encephalitis virus / Strain: TC-83 / References: UniProt: P05674, togavirin

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsParent-ID
1Venezuelan Equine Encephalitis Virus TC-83 StrainVIRUSE1-E2-E3-CP complex. The virus contains 240 copies of E1, E2, and capsid proteins0
2Venezuelan Equine Encephalitis Virus TC83 strain E1 proteinone asymmetric unit of the VEEV contains 4 unique copies of E1, E2, and capsid proteins1
3Venezuelan Equine Encephalitis Virus TC83 strain E2 proteinone asymmetric unit of the VEEV contains 4 unique copies of E1, E2 and capsid proteins1
4Venezuelan Equine Encephalitis Virus TC83 strain capsid proteinone asymmetric unit of the VEEV contains 4 unique copies of E1, E2 and capsid proteins1
Molecular weightValue: 52 MDa / Experimental value: NO
Details of virusEmpty: NO / Enveloped: YES / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Cricetinae / Strain: Baby Hamster Kidney cells
Buffer solutionName: TEN buffer / pH: 7.4 / Details: TEN buffer
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

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Electron microscopy imaging

MicroscopyModel: 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 FIELDBright-field microscopy / Nominal magnification: 100000 X / 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 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 18 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
EM imaging opticsEnergyfilter name: In-column Omega Filter

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Processing

EM software
IDNameCategory
1Rosettamodel fitting
2EMAN3D reconstruction
CTF correctionDetails: CTF parameters were determined from particles within each CCD image
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: projection matching / Resolution: 4.8 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 37000 / Nominal pixel size: 1.07 Å
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, ...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.
Num. of class averages: 3328 / Symmetry type: POINT
Atomic model building
IDProtocolSpaceDetails
1FLEXIBLE FITREALMETHOD--all-atom refinement REFINEMENT PROTOCOL--all-atom refinement against cryo-EM density DETAILS--ROSETTA was used to refine the full-length E1 and E2 and all of the structured part of CP. ROSETTA uses the cryo-EM density as a restraint, along with energy minimization, to eliminate steric clashes and assure proper molecular geometry.
2
3
Atomic model building
IDPDB-ID 3D fitting-ID
13N401
23N402
31EP53
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms31804 0 0 0 31804

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