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Sindbis virion
by single particle (icosahedral) reconstruction, at 7 A resolution
#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 / ID | PORTEIN DATA BANK (PDB) / 3j0f |
|---|---|
| Title | Sindbis virion |
| Descriptor | Capsid protein (E.C.3.4.21.90) E1 envelope glycoprotein E2 envelope glycoprotein |
| Keywords |  VIRUS, alphavirus, virus assembly, glycoprotein |
| Authors | Tang, J., Jose, J., Zhang, W., Chipman, P., Kuhn, R.J., Baker, T.S. |
| Date | Deposition: 2011-07-08, Release: 2011-10-12 |
| PDBj Mine pages |  Summary, Structural Details, Experimental Details, Functional Details |
| Other databases | RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST |
| Structure Visualization | |
| Movies |  Movie 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 viewers |  Yorodumi, jV4, Jmol,  Biological unit (Images, jV) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article Fit: target map of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - primary | |
| Article | J. Mol. Biol., Vol. 414, Issue 3, Page 442-59, Year 2011 |
|---|---|
| Title | Molecular links between the E2 envelope glycoprotein and nucleocapsid core in Sindbis virus. |
| Authors | Jinghua 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. |
| Keywords | Amino 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 |
| Links | PII: S0022-2836(11)01085-0, DOI: 10.1016/j.jmb.2011.09.045, PubMed: 22001018, PMC: PMC3407685 |
 Components | |
| ID 1 : Coat protein, C | |
| Image |   |
|---|---|
| Description | Capsid protein |
| Type | polymer |
| Fragment | UNP residues 1-264 |
| Formula weight | 29410.232 Da |
| Number of molecules | 4 |
| Ec | 3.4.21.90 |
| Source | Method: Isolated from a natural source Common name: SINV NCBI taxonomy: ID:11034Organism scientific: Sindbis virus |
| Links | UniProt: P03316, Sequence view |
| ID 2 : Spike glycoprotein E1 | |
| Image |   |
| Description | E1 envelope glycoprotein |
| Type | polymer |
| Fragment | UNP residues 807-1245 |
| Formula weight | 47417.285 Da |
| Number of molecules | 4 |
| Source | Method: Isolated from a natural source Common name: SINV NCBI taxonomy: ID:11034Organism scientific: Sindbis virus |
| Links | UniProt: P03316, Sequence view |
| ID 3 : Spike glycoprotein E2 | |
| Image |   |
| Description | E2 envelope glycoprotein |
| Type | polymer |
| Fragment | UNP residues 329-751 |
| Formula weight | 46983.086 Da |
| Number of molecules | 4 |
| Source | Method: Isolated from a natural source Common name: SINV NCBI taxonomy: ID:11034Organism scientific: Sindbis virus |
| Links | UniProt: P03316, Sequence view |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Name | sindbis virion |
| Num components | 60 |
| Entity assembly | |
| Name | alphavirus |
| Type | VIRUS |
| Virus entity | |
| Empty | NO |
| Enveloped | YES |
| Virus host category | VERTEBRATES |
| Virus host species | Homo sapiens |
| Virus isolate | STRAIN |
| Virus type | VIRION |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE (CRYO EM) |
| Vitrification | |
| Cryogen name | ETHANE |
 Electron Microscopy | |
| Imaging | |
| Microscope | model: FEI/PHILIPS CM300FEG/T |
|---|---|
| Date | 2001-12-12 |
| Electron gun | |
| Electron source | FIELD EMISSION GUN |
| Accelerating voltage | 300 kV |
| Illumination mode | FLOOD BEAM |
| Lens | |
| Mode | BRIGHT FIELD |
| Detector distance | 0.0 |
| Specimen holder | |
| Specimen holder | model: GATAN LIQUID NITROGEN, type: eucentric |
| Tilt angle | min: 0.0 degrees, max: 0.0 degrees |
| Detector | |
| Type | Kodak SO163 film |
 Processing | |
| Single particle entity | |
| Symmetry type | ICOSAHEDRAL |
|---|---|
| 3D reconstruction | |
| Resolution | 7.0 A |
| 3D fitting | |
| Refinement Space | REAL |
| 3D fitting list | |
| Pdb chain id | A |
| PDB entry ID | 1KXF |
| Refine hist | |
| Total atoms | 4064 |
| Protein atoms | 4064 |
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