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Sindbis virion

by single particle (icosahedral) reconstruction, at 7 A resolution

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

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

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

#4: Depositted structure unit, Made by Jmol

#5: Superimposing with simplified surface model of EM map, EMDB-5251, Made by Jmol

#6: Superimposing with EM 3D map: EMDB-5251, Made by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3j0f
TitleSindbis virion
DescriptorCapsid protein (E.C.3.4.21.90)
E1 envelope glycoprotein
E2 envelope glycoprotein
KeywordsVIRUS, alphavirus, virus assembly, glycoprotein
AuthorsTang, J., Jose, J., Zhang, W., Chipman, P., Kuhn, R.J., Baker, T.S.
DateDeposition: 2011-07-08, Release: 2011-10-12
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, Made by Jmol

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

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

#4: Depositted structure unit, Made by Jmol

#5: Superimposing with simplified surface model of EM map, EMDB-5251, Made by Jmol

#6: Superimposing with EM 3D map: EMDB-5251, Made by UCSF CHIMERA

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

EMDB-5251

CiteFit

Cite: data citing same article

Fit: target map of fitting

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - primary
ArticleJ. Mol. Biol., Vol. 414, Issue 3, Page 442-59, Year 2011
TitleMolecular links between the E2 envelope glycoprotein and nucleocapsid core in Sindbis virus.
AuthorsJinghua Tang, Joyce Jose, Paul Chipman, Wei Zhang, Richard J Kuhn, Timothy S Baker
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, USA.
KeywordsAmino Acid Sequence, Animals, Capsid (chemistry), Cell Line, Cell Membrane (metabolism), Cricetinae, Glycoproteins (chemistry), Hydrophobic and Hydrophilic Interactions, Lipid Bilayers (chemistry), Models, Molecular, Molecular Conformation, Molecular Sequence Data, Nucleocapsid (chemistry), Protein Binding, Protein Conformation, Protein Structure, Tertiary, Viral Envelope Proteins (chemistry), glycoprotein E2, Sindbis virus
LinksPII: S0022-2836(11)01085-0, DOI: 10.1016/j.jmb.2011.09.045, PubMed: 22001018, PMC: PMC3407685
Components
ID 1 : Coat protein, C
Image
DescriptionCapsid protein
Typepolypeptide(L)
FragmentUNP residues 1-264
Formula weight29410.232 Da
Number of molecules4
ID1
Ec3.4.21.90
SourceMethod: Isolated from a natural source
Common name: SINV
NCBI taxonomy: ID:11034
Organism scientific: Sindbis virus
LinksUniProt: P03316, Sequence view
ID 2 : Spike glycoprotein E1
Image
DescriptionE1 envelope glycoprotein
Typepolypeptide(L)
FragmentUNP residues 807-1245
Formula weight47417.285 Da
Number of molecules4
ID2
SourceMethod: Isolated from a natural source
Common name: SINV
NCBI taxonomy: ID:11034
Organism scientific: Sindbis virus
LinksUniProt: P03316, Sequence view
ID 3 : Spike glycoprotein E2
Image
DescriptionE2 envelope glycoprotein
Typepolypeptide(L)
FragmentUNP residues 329-751
Formula weight46983.086 Da
Number of molecules4
ID3
SourceMethod: Isolated from a natural source
Common name: SINV
NCBI taxonomy: ID:11034
Organism scientific: Sindbis virus
LinksUniProt: P03316, Sequence view
Sample
Assembly
Aggregation statePARTICLE
Namesindbis virion
Num components60
Entity assembly
Assembly-ID1
Namealphavirus
TypeVIRUS
Virus entity
EmptyNO
EnvelopedYES
Virus host categoryVERTEBRATES
Virus host speciesHomo sapiens
Virus isolateSTRAIN
Virus typeVIRION
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Vitrification
Cryogen nameETHANE
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI/PHILIPS CM300FEG/T
Date2001-12-12
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
Detector distance0.0
Specimen holder
Specimen holderModel: GATAN LIQUID NITROGEN, Type: eucentric
Tilt angleMin: 0.0 degrees, Max: 0.0 degrees
Detector
TypeKodak SO163 film
Processing
Single particle entity
Symmetry typeICOSAHEDRAL
3D reconstruction
Resolution7.0 A
3D fitting
Refinement SpaceREAL
3D fitting list
3D Fitting ID1
Pdb chain idA
PDB entry ID1KXF
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms4064
Protein atoms4064
Download
PDB format
Allpdb3j0f.ent.gz
pdb3j0f.ent (uncompressed file)
Header onlypdb3j0f.ent.gz
mmCIF format
mmCIF3j0f.cif.gz
XML format
All3j0f.xml.gz
No-atom3j0f-noatom.xml.gz
Ext-atom3j0f-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.9 MB
.webm (WebM/VP8 format), 5.6 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.3 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.1 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 2.9 MB
.webm (WebM/VP8 format), 3.8 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.5 MB
movie #6
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5 MB