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CRYOEM MODEL OF THE VESICULAR STOMATITIS VIRUS

by helical reconstruction, at 10.6 A resolution

Movie

Orientation:

#1: Biological unit as representative helical assembly, Image by Jmol

#2: Depositted structure unit, Image by Jmol

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 2wyy
TitleCRYOEM MODEL OF THE VESICULAR STOMATITIS VIRUS
DescriptorNUCLEOPROTEIN
KeywordsVIRUS, RNA, NSRV, HELIX, VIRION, VIRAL NUCLEOPROTEIN
AuthorsGe, P., Tsao, J., Green, T.J., Luo, M., Zhou, Z.H.
DateDeposition: 2009-11-20, Release: 2010-02-16
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Biological unit as representative helical assembly, Image by Jmol

#2: Depositted structure unit, Image by Jmol

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries

EMDB-1663

CiteFit

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Fit: target map of fitting

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Article
Citation - primary
ArticleScience, Vol. 327, Issue 5966, Page 689-93, Year 2010
TitleCryo-EM model of the bullet-shaped vesicular stomatitis virus.
AuthorsPeng 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.
KeywordsCryoelectron 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
LinksDOI: 10.1126/science.1181766, PubMed: 20133572, PMC: PMC2892700
Components
ID 1 : NUCLEOCAPSID PROTEIN, NP, PROTEIN N
Image
DescriptionNUCLEOPROTEIN
Typepolypeptide(L)
Formula weight47464.406 Da
Number of molecules10
ID1
SourceMethod: Isolated from a natural source
Common name: VSV
Cell line: BHK
NCBI taxonomy: ID:11285
Organism scientific: VESICULAR STOMATITIS INDIANA VIRUS
Strain: SAN JUAN
LinksUniProt: P03521, Sequence view
ID 2 : POLY-URIDINE
Image
DescriptionPOLY-URIDINE
Typepolyribonucleotide
Formula weight13732.619 Da
Number of molecules2
ID2
SourceMethod: Obtained synthetically
LinksSequence view
Sample
Assembly
Aggregation stateFILAMENT
NameVSV (INDIANA)
Assembly
DetailsDATA AQUISITION
Buffer
Name100MM NACL, 10NM TRIS, 1MM EDTA
Experiment
Reconstruction methodHELICAL
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.4
Vitrification
DetailsCRYOGEN - ETHANE, HUMIDITY - 50, TEMPERATURE - 80, INSTRUMENT - MANUAL PLUNGER, METHOD- MANUAL BLOT 1 SECOND BEFORE PLUNGING, DETAILS - VITRIFICATION CARRIED OUT IN OPEN ROOM.
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
Date2007-01-05
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Electron dose20 e/A**2
Illumination modeSPOT SCAN
Lens
MagnificationCalibrated: 98000 X, Nominal: 59000 X
CsNominal: 2 mm
Nominal defocusMax: 2500 nm, Min: 800 nm
Specimen holder
Temperature80 Kelvin
Detector
TypeTIETZ CCD
Image scans
Number digital images212
Processing
2D projection selection
Software nameEMAN
3D reconstruction
DetailsSUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1663.
MethodPROJECTION MATCHING
Resolution10.6 A
3D fitting
MethodRIGID BODY
Refinement ProtocolRIGID BODY REFINEMENT
Refinement SpaceREAL
Target criteriaCROSS-CORRELATION
3D fitting list
3D Fitting ID1
Refine
Refine idELECTRON MICROSCOPY
Ls d res high10.00 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high10.00
Total atoms34620
Nucleic acid atoms1800
Protein atoms32820
Download
PDB format
Allpdb2wyy.ent.gz
pdb2wyy.ent (uncompressed file)
Header onlypdb2wyy.ent.gz
mmCIF format
mmCIF2wyy.cif.gz
XML format
All2wyy.xml.gz
No-atom2wyy-noatom.xml.gz
Ext-atom2wyy-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.3 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 2.6 MB
.webm (WebM/VP8 format), 3.5 MB