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The structure of immature Yellow Fever virus particle

by single particle (icosahedral) reconstruction

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#1: Biological unit as complete icosahedral assembly, Image by Jmol

#2: Biological unit as icosahedral pentamer, Image by Jmol

#3: Biological unit as icosahedral 23 hexamer, Image by Jmol

#4: Depositted structure unit, Image by Jmol

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 1na4
TitleThe structure of immature Yellow Fever virus particle
Descriptormajor envelope protein E
KeywordsVirus, flavivirus, flaviviridae, yellow fever immature virus, prM particle, Icosahedral virus
AuthorsZhang, Y., Corver, J., Chipman, P.R., Lenches, E., Zhang, W., Pletnev, S.V., Sedlak, D., Baker, T.S., Strauss, J.H., Kuhn, R.J., Rossmann, M.G.
DateDeposition: 2002-11-26, Release: 2003-12-09
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
MoviesMovie Page

#1: Biological unit as complete icosahedral assembly, Image by Jmol

#2: Biological unit as icosahedral pentamer, Image by Jmol

#3: Biological unit as icosahedral 23 hexamer, Image by Jmol

#4: Depositted structure unit, Image by Jmol

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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Article
Citation - primary
ArticleEMBO J., Vol. 22, Issue 11, Page 2604-13, Year 2003
TitleStructures of immature flavivirus particles.
AuthorsYing Zhang, Jeroen Corver, Paul R Chipman, Wei Zhang, Sergei V Pletnev, Dagmar Sedlak, Timothy S Baker, James H Strauss, Richard J Kuhn, Michael G Rossmann
Department of Biological Sciences, Lilly Hall, 915 West State Street, Purdue University, West Lafayette, IN 47907-2054, USA.
KeywordsAnimals, Cell Line, Cryoelectron Microscopy, Dengue Virus (chemistry), Flavivirus (chemistry), Image Processing, Computer-Assisted, Lipid Bilayers (chemistry), Models, Molecular, Nucleocapsid (chemistry), Sindbis Virus (chemistry), Viral Proteins (chemistry), Yellow fever virus (chemistry)
LinksPubMed: 12773377, DOI: 10.1093/emboj/cdg270, PMC: PMC156766
Components
ID 1 : major envelope protein E
Image
Descriptionmajor envelope protein E
Typepolypeptide(L)
Formula weight43231.574 Da
Number of molecules3
ID1
SourceMethod: Isolated from a natural source
Genus: Flavivirus
NCBI taxonomy: ID:11089
Organism scientific: Yellow fever virus
LinksUniProt: P14336, Sequence view
Sample
Assembly
Aggregation statePARTICLE
DetailsThe samples were produced by adding ammonium chloride to the medium in the late infection stage.
NameYellow fever immature virus
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Processing
2D projection selection
Software nameEMFIT
Single particle entity
Symmetry typeICOSAHEDRAL
3D fitting
Refinement SpaceREAL
Software nameEMFIT
3D fitting list
3D Fitting ID1
PDB entry ID1SVB
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms1185
Protein atoms1185
Download
PDB format
Allpdb1na4.ent.gz
pdb1na4.ent (uncompressed file)
Header onlypdb1na4.ent.gz
mmCIF format
mmCIF1na4.cif.gz
XML format
All1na4.xml.gz
No-atom1na4-noatom.xml.gz
Ext-atom1na4-extatom.xml.gz
Movie files
movie #1
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movie #2
.mp4 (H.264/MPEG-4 AVC format), 2.9 MB
.webm (WebM/VP8 format), 3.8 MB
movie #3
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.webm (WebM/VP8 format), 3.8 MB
movie #4
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.webm (WebM/VP8 format), 3.4 MB