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Atomic CryoEM Structure of a Nonenveloped Virus Suggests How Membrane Penetration Protein is Primed for Cell Entry
by single particle (icosahedral) reconstruction, at 3.3 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-5160, Made by Jmol
#6: Superimposing with EM 3D map: EMDB-5160, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | PORTEIN DATA BANK (PDB) / 3iyl |
|---|---|
| Title | Atomic CryoEM Structure of a Nonenveloped Virus Suggests How Membrane Penetration Protein is Primed for Cell Entry |
| Descriptor | Outer capsid VP4 Core protein VP6 VP1 VP3 |
| Keywords |  VIRUS, Non-enveloped virus, Membrane penetration protein, Autocleavage, Myristol Group, Icosahedral virus |
| 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-5160, Made by Jmol #6: Superimposing with EM 3D map: EMDB-5160, Made by UCSF CHIMERA |
| Structure viewers |  Yorodumi, jV4, Jmol,  Biological unit (Images, jV) |
| Related Structure Data | |
| Related Entries |
Fit: target map of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - primary | |
| Article | Cell(Cambridge,Mass.), Vol. 141, Page: 472 - 482, Year: 2010, |
|---|---|
| Title | 3.3 A cryo-EM structure of a nonenveloped virus reveals a priming mechanism for cell entry. |
| Authors | Zhang, X., Jin, L., Fang, Q., Hui, W.H., Zhou, Z.H. |
| Links | DOI: 10.1016/j.cell.2010.03.041 |
 Components | |
| ID 1 : Outer capsid VP4 | |
| Image |   |
|---|---|
| Description | Outer capsid VP4 |
| Type | polypeptide(L) |
| Formula weight | 68647.539 Da |
| Number of molecules | 20 |
| ID | 1 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:128987Organism scientific: Grass carp reovirus |
| Links | UniProt: Q8JU67, Sequence view |
| ID 2 : Core protein VP6 | |
| Image |   |
| Description | Core protein VP6 |
| Type | polypeptide(L) |
| Formula weight | 44606.980 Da |
| Number of molecules | 2 |
| ID | 2 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:128987Organism scientific: Grass carp reovirus |
| Links | UniProt: Q8JU64, Sequence view |
| ID 3 : VP1 | |
| Image |   |
| Description | VP1 |
| Type | polypeptide(L) |
| Formula weight | 141513.016 Da |
| Number of molecules | 1 |
| ID | 3 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:128987Organism scientific: Grass carp reovirus |
| Links | UniProt: Q9E3W0, Sequence view |
| ID 4 : VP3 | |
| Image |   |
| Description | VP3 |
| Type | polypeptide(L) |
| Formula weight | 132204.203 Da |
| Number of molecules | 2 |
| ID | 4 |
| Source | Method: Isolated from a natural source NCBI taxonomy: ID:128987Organism scientific: Grass carp reovirus |
| Links | UniProt: Q9E3V8, Sequence view |
| ID 5 : MYRISTIC ACID | |
| Image |    |
| Description | MYRISTIC ACID |
| Type | non-polymer |
| Formula weight | 228.374 Da |
| Number of molecules | 10 |
| ID | 5 |
| Source | Method: Obtained synthetically |
 Sample | |
| Assembly | |
| Aggregation state | PARTICLE |
|---|---|
| Details | The sample was monodisperse |
| Experimental Mass | 72 |
| Theoretical Mass | 72 |
| Name | Aquareovirus |
| Num components | 4 |
| Entity assembly | |
| Assembly-ID | 1 |
| Name | Aquareovirus |
| Type | VIRUS |
| Virus entity | |
| Empty | NO |
| Enveloped | NO |
| Virus host category | VERTEBRATES |
| Virus isolate | STRAIN |
| Virus type | OTHER |
| Experiment | |
| Reconstruction method | SINGLE PARTICLE |
| Specimen type | VITREOUS ICE (CRYO EM) |
| Sample preparation | |
| Details | 10mM PBS Buffer |
| pH | 7.5 |
| Vitrification | |
| Cryogen name | METHANE |
| Humidity | 100 |
| Instrument | FEI Vitrobot |
| Method | Blot for 7-9 seconds before plunging |
| Temp | 90 Kelvin |
| Experiment | |
| Method | ELECTRON MICROSCOPY |
 Electron Microscopy | |
| Imaging | |
| Microscope | Model: OTHER |
|---|---|
| Date | Mar-2009 |
| Electron gun | |
| Electron source | FIELD EMISSION GUN |
| Accelerating voltage | 300 kV |
| Electron dose | 25 e/A**2 |
| Illumination mode | FLOOD BEAM |
| Lens | |
| Mode | BRIGHT FIELD |
| Magnification | Calibrated: 57700 X, Nominal: 59000 X |
| Cs | Nominal: 2.7 mm |
| Astigmatism | objective lens astigmatism was corrected at 250,000 times magnification |
| Detector distance | 0.0 |
| Nominal defocus | Max: 2700 nm, Min: 400 nm |
| Specimen holder | |
| Specimen holder | Model: OTHER, Type: Eucentric |
| Tilt angle | Min: 0.0 degrees, Max: 0.0 degrees |
| Temperature | 90 Kelvin |
| Recording temperature | Minimum: 90 |
| Detector | |
| Type | Kodak SO163 film |
 Processing | |
| Single particle entity | |
| Symmetry type | ICOSAHEDRAL |
|---|---|
| 3D reconstruction | |
| CTF correction method | Each particle |
| Euler angles details | Frealign IMIRS |
| Method | Fourier Space Reconstruction |
| Number of particles | 18464 |
| Resolution | 3.3 A |
| Resolution method | FSC at 0.143 cut-off |
| Software | Frealign IMIRS |
| Refine hist | |
| Cycle id | LAST |
| Refine id | ELECTRON MICROSCOPY |
| Total atoms | 80985 |
| Ligand atoms | 150 |
| Protein atoms | 80835 |
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