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

by single particle (icosahedral) reconstruction, at 4.8 A resolution

Movie

Orientation:

#1: Biological unit as complete icosahedral assembly, Image by Jmol

#2: Biological unit as icosahedral pentamer, Image by Jmol

#3: Biological unit as icosahedral 23 hexamer, Image by Jmol

#4: Depositted structure unit, Image by Jmol

#5: Superimposing with simplified surface model of EM map, EMDB-5275, Image by Jmol

#6: With PDB-3j0c, Image by Jmol

#7: Superimposing with EM 3D map: EMDB-5275 (with PDB-3j0c), Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 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
AuthorsZhang, R., Hryc, C.F., Chiu, W.
DateDeposition: 2011-07-21, Release: 2011-08-24
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Biological unit as complete icosahedral assembly, Image by Jmol

#2: Biological unit as icosahedral pentamer, Image by Jmol

#3: Biological unit as icosahedral 23 hexamer, Image by Jmol

#4: Depositted structure unit, Image by Jmol

#5: Superimposing with simplified surface model of EM map, EMDB-5275, Image by Jmol

#6: With PDB-3j0c, Image by Jmol

#7: Superimposing with EM 3D map: EMDB-5275 (with PDB-3j0c), Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries

EMDB-5275

CiteFit

EMDB-5276

CiteFit

Cite: data citing same article

Fit: target map of fitting

Article
Citation - primary
ArticleEMBO J., Vol. 30, Issue 18, Page 3854-63, Year 2011
Title4.4 Å cryo-EM structure of an enveloped alphavirus Venezuelan equine encephalitis virus.
AuthorsRui Zhang, Corey F Hryc, Yao Cong, Xiangan Liu, Joanita Jakana, Rodion Gorchakov, Matthew L Baker, Scott C Weaver, Wah Chiu
Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, USA.
KeywordsAnimals, Cryoelectron Microscopy, Encephalitis Virus, Venezuelan Equine (ultrastructure), Horses, Models, Molecular, Viral Proteins (ultrastructure), Viral Vaccines, Virion (ultrastructure), Virulence
LinksDOI: 10.1038/emboj.2011.261, PubMed: 21829169, PMC: PMC3173789
Components
ID 1 : Spike glycoprotein E3
Image
DescriptionE3 protein
Typepolypeptide(L)
FragmentUNP residues 276-334
Formula weight6488.640 Da
Number of molecules4
ID1
SourceMethod: Isolated from a natural source
Common name: VEEV
Details: purified from infected Baby hamster kidney (BHK) cells
NCBI taxonomy: ID:11037
Organism scientific: Venezuelan equine encephalitis virus
Strain: TC-83
LinksUniProt: P05674, Sequence view
Sample
Assembly
Aggregation statePARTICLE
DetailsThe virus contains 240 copies of E1, E2, E3 and capsid proteins
NameVenezuelan Equine Encephalitis Virus TC-83 Strain
Entity assembly
Assembly-ID1
NameVenezuelan Equine Encephalitis Virus TC83 strain E3 protein that is cleaved from p62 protein
Virus entity
EmptyNO
EnvelopedYES
Ictvdb id00.073.0.01
Virus host categoryVERTEBRATES
Virus host growth cellBaby Hamster Kidney cells
Virus host speciesEquus
Virus isolateSTRAIN
Virus typeVIRION
Buffer
NameTEN buffer
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.4
Sample support
Detailstwo of the eight grids used for imaging contained continuous carbon film underneath the samples
Vitrification
Cryogen nameETHANE
Detailsvitrification carried out in Chiu lab, Houston, TX
Humidity100
InstrumentVitrobot (FEI Inc)
Method2 blots, each blot 2 second before plunging, offset = 0
Temp89.34 Kelvin
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: JEOL 3200FSC
Date2008-04-09
Detailsomega energy filter
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Electron dose18 e/A**2
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationNominal: 100000 X
CsNominal: 4.3 mm
Astigmatismobjective lens astigmatism was corrected at 100,000 times magnification
Nominal defocusMax: 2500 nm, Min: 400 nm
Energy filterOmega Filter
Specimen holder
Specimen holderModel: JEM3200FSC CRYOHOLDER, Type: Eucentric
Tilt angleMin: 0.0 degrees, Max: 0.0 degrees
Temperature96 Kelvin
Detector
TypeGatan 4kx4k CCD Camera
Processing
2D projection selection
Software nameCHIMERA
Single particle entity
Symmetry typeICOSAHEDRAL
3D reconstruction
CTF correction methodCTF parameters were determined from particles within each CCD image
DetailsAfter 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 detailsThe 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).
Methodprojection matching
Nominal pixel size1.07 A/pix
Num class averages3328
Number of particles37000
Resolution4.8 A
SoftwareEMAN
3D fitting
DetailsThe E3 homology model was not further refined against the cryo-EM density map due to its less-resolved quality
Methodrigid-body fitting
Refinement SpaceREAL
Software nameCHIMERA
3D fitting list
3D Fitting ID1
PDB entry ID3N40
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms1800
Protein atoms1800
Download
PDB format
Allpdb3j0g.ent.gz
pdb3j0g.ent (uncompressed file)
Header onlypdb3j0g.ent.gz
mmCIF format
mmCIF3j0g.cif.gz
XML format
All3j0g.xml.gz
No-atom3j0g-noatom.xml.gz
Ext-atom3j0g-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 3.9 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 2.9 MB
.webm (WebM/VP8 format), 3.8 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 2.2 MB
.webm (WebM/VP8 format), 3.1 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 2.8 MB
.webm (WebM/VP8 format), 3.8 MB
movie #6
.mp4 (H.264/MPEG-4 AVC format), 2.6 MB
.webm (WebM/VP8 format), 3.5 MB
movie #7
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.3 MB