PDB-2wyy: CRYOEM MODEL OF THE VESICULAR STOMATITIS VIRUS

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 2wyy
Title	CRYOEM MODEL OF THE VESICULAR STOMATITIS VIRUS
Descriptor	NUCLEOPROTEIN
Keywords	VIRUS, RNA, NSRV, HELIX, VIRION, VIRAL NUCLEOPROTEIN
Authors	Ge, P., Tsao, J., Green, T.J., Luo, M., Zhou, Z.H.
Date	Deposition: 2009-11-20, Release: 2010-02-16
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 representative helical assembly, Made by Jmol #2: Depositted structure unit, Made by Jmol
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1663 CiteFit PDB-1fzj PDB-1fzm Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram EMDB-5128 EMDB-5129 PDB-3iky PDB-3j04 PDB-3g37 List of similar structure data about Omokage system

Article
Citation - primary
Article	Science, Vol. 327, Issue 5966, Page 689-93, 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 Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles (UCLA), Los Angeles, CA 90095-7364, USA.
Keywords	Cryoelectron Microscopy, Crystallography, X-Ray, Image Processing, Computer-Assisted, Lipid Bilayers, M protein, Vesicular stomatitis virus, Models, Molecular, Mutagenesis, Nucleocapsid Proteins (chemistry), Protein Conformation, Protein Structure, Secondary, Protein Structure, Tertiary, Protein Subunits (chemistry), RNA, Viral (chemistry), Vesiculovirus (chemistry), Viral Matrix Proteins (chemistry), Virion (chemistry), Virus Assembly
Links	DOI: 10.1126/science.1181766, PubMed: 20133572, PMC: PMC2892700

Components
ID 1 : NUCLEOCAPSID PROTEIN, NP, PROTEIN N
Image
Description	NUCLEOPROTEIN
Type	polymer
Formula weight	47464.406 Da
Number of molecules	10
Source	Method: Isolated from a natural source Common name: VSV Cell line: BHK NCBI taxonomy: ID:11285 Organism scientific: VESICULAR STOMATITIS INDIANA VIRUS Strain: SAN JUAN
Links	UniProt: P03521, Sequence view
ID 2 : POLY-URIDINE
Image
Description	POLY-URIDINE
Type	polymer
Formula weight	13732.619 Da
Number of molecules	2
Source	Method: Obtained synthetically
Links	Sequence view

Sample
Assembly
Aggregation state	FILAMENT
Name	VSV (INDIANA)
Assembly
Details	DATA AQUISITION
Buffer
Name	100MM NACL, 10NM TRIS, 1MM EDTA
Experiment
Reconstruction method	HELICAL
Specimen type	VITREOUS ICE (CRYO EM)
Sample preparation
pH	7.4
Vitrification
Details	CRYOGEN - ETHANE, HUMIDITY - 50, TEMPERATURE - 80, INSTRUMENT - MANUAL PLUNGER, METHOD- MANUAL BLOT 1 SECOND BEFORE PLUNGING, DETAILS - VITRIFICATION CARRIED OUT IN OPEN ROOM.

Processing
2D projection selection
Software name	EMAN
3D reconstruction
Details	SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1663.
Method	PROJECTION MATCHING
Resolution	10.6 A
3D fitting
Method	RIGID BODY
Refinement Protocol	RIGID BODY REFINEMENT
Refinement Space	REAL
Target criteria	CROSS-CORRELATION
Refine
Ls d res high	10.00 A
ID	1
Refine hist
D res high	10.00
Total atoms	34620
Nucleic acid atoms	1800
Protein atoms	32820