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Pseudo-atomic structure of the E2-E1 protein shell in Sindbis virus
by single particle (icosahedral) reconstruction, at 9 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-1121, Made by Jmol
#6: Superimposing with EM 3D map: EMDB-1121, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 3muw |
|---|---|
| Title | Pseudo-atomic structure of the E2-E1 protein shell in Sindbis virus |
| Descriptor | Structural polyprotein (E.C.3.4.21.-) |
| Keywords |  VIRUS, icosahedral protein shell, icosahedral virus |
| Authors | Li, L., Jose, J., Xiang, Y., Kuhn, R.J., Rossmann, M.G. |
| Date | Deposition: 2010-05-03, Release: 2010-11-24 |
| 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-1121, Made by Jmol #6: Superimposing with EM 3D map: EMDB-1121, 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 | Nature, Vol. 468, Issue 7324, Page 705-8, Year 2010 |
|---|---|
| Title | Structural changes of envelope proteins during alphavirus fusion. |
| Authors | Long Li, Joyce Jose, Ye Xiang, Richard J Kuhn, Michael G Rossmann Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, Indiana 47907-2054, USA. |
| Keywords | Animals, Cell Line, Cryoelectron Microscopy, Crystallography, X-Ray, Drosophila melanogaster, Endosomes (metabolism), Hydrogen-Ion Concentration, Hydrophobic and Hydrophilic Interactions, Membrane Fusion, Membrane Glycoproteins (chemistry), Models, Molecular, Protein Multimerization, Protein Structure, Quaternary, Protein Structure, Tertiary, Receptors, Virus (metabolism), Sindbis Virus (chemistry), Viral Envelope Proteins (chemistry), Viral Fusion Proteins (chemistry), Virion (chemistry), Virus Internalization, glycoprotein E1, Sindbis virus, glycoprotein E2, Sindbis virus |
| Links | DOI: 10.1038/nature09546, PubMed: 21124457, PMC: PMC3057476 |
 Components | |
| ID 1 : p130, Capsid protein, Coat protein, C, p62, E3/E2, E3 protein, Spike glycoprotein E3, E2 envelope glycoprotein, Spike glycoprotein E2, 6K protein, E1 envelope glycoprotein, Spike glycoprotein E1 | |
| Image |   |
|---|---|
| Description | Structural polyprotein |
| Type | polymer |
| Formula weight | 41312.125 Da |
| Number of molecules | 4 |
| Ec | 3.4.21.- |
| Source | Method: Isolated from a natural source Common name: SINV NCBI taxonomy: ID:11034Organism scientific: Sindbis virus Strain: Toto64 |
| Links | UniProt: P03316, Sequence view |
| ID 2 : p130, Capsid protein, Coat protein, C, p62, E3/E2, E3 protein, Spike glycoprotein E3, E2 envelope glycoprotein, Spike glycoprotein E2, 6K protein, E1 envelope glycoprotein, Spike glycoprotein E1 | |
| Image |   |
| Description | Structural polyprotein |
| Type | polymer |
| Formula weight | 38509.012 Da |
| Number of molecules | 4 |
| Ec | 3.4.21.- |
| Source | Method: Isolated from a natural source Common name: SINV NCBI taxonomy: ID:11034Organism scientific: Sindbis virus Strain: Toto64 |
| Links | UniProt: P03316, Sequence view |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Name | Sindbis virus |
| Entity assembly | |
| Name | E2-E1 protein shell of Sindbis virus |
| Virus entity | |
| Ictvdb id | Toto64 |
| Virus host category | VERTEBRATES |
| Virus host growth cell | BHK cell |
| Virus host species | homo sapiens |
| Virus isolate | STRAIN |
| Virus type | Virion |
| Buffer | |
| Name | TNE buffer |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE (CRYO EM) |
| Sample preparation | |
| pH | 7.5 |
| Sample concentration | 5 mg/ml |
| Sample support | |
| Details | This grid plus sample was kept at 100 K |
 Electron Microscopy | |
| Imaging | |
| Microscope | model: FEI/PHILIPS CM200T |
|---|---|
| Date | 2000-06-21 |
| Electron gun | |
| Electron source | FIELD EMISSION GUN |
| Accelerating voltage | 200 kV |
| Electron dose | 18 e/A**2 |
| Illumination mode | FLOOD BEAM |
| Lens | |
| Mode | BRIGHT FIELD |
| Magnification | calibrated: 39220 X, nominal: 38000 X |
| Cs | nominal: 2.0 mm |
| Nominal defocus | max: 2580 nm, min: 1100 nm |
| Specimen holder | |
| Tilt angle | min: 0 degrees, max: 0 degrees |
| Detector | |
| Type | Kodak SO163 film |
 Processing | |
| 2D projection selection | |
| Number of particles | 7085 |
|---|---|
| Software name | EMfit |
| Single particle entity | |
| Symmetry type | ICOSAHEDRAL |
| 3D reconstruction | |
| CTF correction method | CTF correction of each particle. |
| Method | model-based common lines |
| Resolution | 9.0 A |
| 3D fitting | |
| Refinement Protocol | rigid body |
| Refinement Space | REAL |
| Software name | EMfit |
| Target criteria | sumf |
| Refine hist | |
| Total atoms | 2468 |
| Protein atoms | 2468 |
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