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VP7 recoated rotavirus DLP
by single particle (icosahedral) reconstruction, at 3.8 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-1571, Made by Jmol
#6: With PDB-3gzt, Made by Jmol
#7: Superimposing with EM 3D map: EMDB-1571 (with PDB-3gzt), Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 3gzu |
|---|---|
| Title | VP7 recoated rotavirus DLP |
| Descriptor | Inner capsid protein VP2 Intermediate capsid protein VP6 |
| Keywords |  VIRUS, rotavirus, VP7, VP6, VP2, 7RP, DLP, Capsid protein, Metal-binding, Virion, Core protein, RNA-binding, Icosaderal virus |
| Authors | Chen, J.Z., Settembre, E.C., Harrison, S.C., Grigorieff, N. |
| Date | Deposition: 2009-04-07, Release: 2009-07-14 |
| 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-1571, Made by Jmol #6: With PDB-3gzt, Made by Jmol #7: Superimposing with EM 3D map: EMDB-1571 (with PDB-3gzt), 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 | Proc. Natl. Acad. Sci. U.S.A., Vol. 106, Issue 26, Page 10644-8, Year 2009 |
|---|---|
| Title | Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM. |
| Authors | James Z Chen, Ethan C Settembre, Scott T Aoki, Xing Zhang, A Richard Bellamy, Philip R Dormitzer, Stephen C Harrison, Nikolaus Grigorieff Rosenstiel Basic Medical Research Center, Brandeis University, Waltham, MA 02454, USA. |
| Keywords | Antigens, Viral (chemistry), Calcium (metabolism, 7440-70-2), Capsid Proteins (chemistry), Cryoelectron Microscopy (methods), Crystallography, X-Ray, Models, Biological, Models, Molecular, Protein Multimerization, Protein Structure, Quaternary, Rotavirus (metabolism), VP1 protein, Rotavirus, VP2 protein, Rotavirus, VP3 protein, Rotavirus, VP7 protein, Rotavirus, Viral Core Proteins (chemistry), Virion (metabolism) |
| Links | DOI: 10.1073/pnas.0904024106, PubMed: 19487668, PMC: PMC2689313 |
 Components | |
| ID 1 : Inner capsid protein VP2 | |
| Image |   |
|---|---|
| Description | Inner capsid protein VP2 |
| Type | polymer |
| Fragment | VP2 |
| Formula weight | 93128.227 Da |
| Number of molecules | 2 |
| Source | Method: Isolated from a genetically manipulated source Gene: RV-A, ID:28875, Rotavirus AHost: ID:7108, Spodoptera frugiperda, Bac-to-Bac |
| Links | UniProt: B2BMF8, Sequence view |
| ID 2 : Intermediate capsid protein VP6 | |
| Image |   |
| Description | Intermediate capsid protein VP6 |
| Type | polymer |
| Fragment | VP6 |
| Formula weight | 44880.117 Da |
| Number of molecules | 13 |
| Source | Method: Isolated from a genetically manipulated source Gene: ID:10969, Rhesus RotavirusHost: ID:7108, Spodoptera frugiperda, Sf9, Bac-to-Bac |
| Links | UniProt: P04509, Sequence view |
| ID 3 : ZINC ION | |
| Image |    |
| Description | ZINC ION |
| Type | non-polymer |
| Formula weight | 65.380 Da |
| Number of molecules | 5 |
| Source | Method: Obtained synthetically |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Name | VP7 recoated rotavirus DLP |
| Entity assembly | |
| Details | capsid protein VP7. VP6 and VP2 |
| Name | VP7 recoated rotavirus DLP |
| Virus entity | |
| Virus host category | Reoviridae |
| Virus host species | Bovine |
| Virus type | Double-layered-particle |
| Buffer | |
| Name | 20mM TrisHCl, 50mM NaCl, 2mM CaCl2 |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE (CRYO EM) |
| Sample preparation | |
| pH | 8.0 |
| Sample concentration | 5.0 mg/ml |
| Sample support | |
| Details | C-flat grids |
| Vitrification | |
| Details | manual plunging at 90K |
 Electron Microscopy | |
| Imaging | |
| Microscope | model: TF30 |
|---|---|
| Date | 2007-12-01 |
| Electron gun | |
| Electron source | FEG |
| Accelerating voltage | 300 kV |
| Electron dose | 2500 e/A**2 |
| Illumination mode | flood beam |
| Lens | |
| Mode | bright field |
| Magnification | calibrated: 58168 X, nominal: 59000 X |
| Cs | nominal: 2.0 mm |
| Nominal defocus | max: 3500 nm, min: 1200 nm |
| Specimen holder | |
| Tilt angle | min: 0 degrees, max: 0 degrees |
| Temperature | 90 Kelvin |
| Detector | |
| Details | Kodak ISO163 |
| Type | film |
 Processing | |
| Single particle entity | |
| Symmetry type | ICOSAHEDRAL |
|---|---|
| 3D reconstruction | |
| Actual pixel size | 1.233 A/pix |
| CTF correction method | individual particle CTF |
| Details | projection matching by FREALIGN |
| Magnification calibration | 58168 |
| Method | projection matching and refinement using FEALIGN |
| Nominal pixel size | 1.233 A/pix |
| Resolution | 3.8 A |
| 3D fitting | |
| Refinement Space | REAL |
| Refine hist | |
| Total atoms | 53987 |
| Ligand atoms | 5 |
| Protein atoms | 53982 |
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