+Open data
-Basic information
Entry | Database: PDB / ID: 2wyy | ||||||
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Title | CRYOEM MODEL OF THE VESICULAR STOMATITIS VIRUS | ||||||
Components |
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Keywords | VIRUS / RNA / NSRV / HELIX / VIRION / VIRAL NUCLEOPROTEIN | ||||||
Function / homology | Function and homology information RNA replication / helical viral capsid / viral transcription / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding Similarity search - Function | ||||||
Biological species | VESICULAR STOMATITIS INDIANA VIRUS | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 10.6 Å | ||||||
Authors | Ge, P. / Tsao, J. / Green, T.J. / Luo, M. / Zhou, Z.H. | ||||||
Citation | Journal: Science / Year: 2010 Title: Cryo-EM model of the bullet-shaped vesicular stomatitis virus. Authors: Peng Ge / Jun Tsao / Stan Schein / Todd J Green / Ming Luo / Z Hong Zhou / Abstract: Vesicular stomatitis virus (VSV) is a bullet-shaped rhabdovirus and a model system of negative-strand RNA viruses. Through direct visualization by means of cryo-electron microscopy, we show that each ...Vesicular stomatitis virus (VSV) is a bullet-shaped rhabdovirus and a model system of negative-strand RNA viruses. Through direct visualization by means of cryo-electron microscopy, we show that each virion contains two nested, left-handed helices: an outer helix of matrix protein M and an inner helix of nucleoprotein N and RNA. M has a hub domain with four contact sites that link to neighboring M and N subunits, providing rigidity by clamping adjacent turns of the nucleocapsid. Side-by-side interactions between neighboring N subunits are critical for the nucleocapsid to form a bullet shape, and structure-based mutagenesis results support this description. Together, our data suggest a mechanism of VSV assembly in which the nucleocapsid spirals from the tip to become the helical trunk, both subsequently framed and rigidified by the M layer. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 2wyy.cif.gz | 763.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wyy.ent.gz | 627.8 KB | Display | PDB format |
PDBx/mmJSON format | 2wyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wyy_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2wyy_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2wyy_validation.xml.gz | 99.3 KB | Display | |
Data in CIF | 2wyy_validation.cif.gz | 167.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/2wyy ftp://data.pdbj.org/pub/pdb/validation_reports/wy/2wyy | HTTPS FTP |
-Related structure data
Related structure data | 1663MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 15 / Rise per n subunits: 6.981 Å / Rotation per n subunits: -48 °) |
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given / Matrix: (0.669131, -0.743145), |
-Components
#1: Protein | Mass: 47463.949 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) VESICULAR STOMATITIS INDIANA VIRUS / Strain: SAN JUAN / References: UniProt: P03521 #2: RNA chain | Mass: 13732.498 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) VESICULAR STOMATITIS INDIANA VIRUS / Strain: SAN JUAN |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: VSV (INDIANA) / Type: VIRUS |
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Buffer solution | Name: 100MM NACL, 10NM TRIS, 1MM EDTA / pH: 7.4 / Details: 100MM NACL, 10NM TRIS, 1MM EDTA |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE Details: CRYOGEN - ETHANE, HUMIDITY - 50, TEMPERATURE - 80, INSTRUMENT - MANUAL PLUNGER, METHOD- MANUAL BLOT 1 SECOND BEFORE PLUNGING, DETAILS - VITRIFICATION CARRIED OUT IN OPEN ROOM. |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 / Date: Jan 5, 2007 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 98000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2 mm |
Specimen holder | Temperature: 80 K |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: GENERIC TVIPS |
Image scans | Num. digital images: 212 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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3D reconstruction | Method: PROJECTION MATCHING / Resolution: 10.6 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1663. Symmetry type: HELICAL | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--RIGID BODY REFINEMENT | ||||||||||||
Atomic model building | PDB-ID: 2WYY Accession code: 2WYY / Source name: PDB / Type: experimental model | ||||||||||||
Refinement | Highest resolution: 10.6 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 10 Å
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