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Low pH Immature Dengue Virus

by single particle (icosahedral) reconstruction, at 25 A resolution

Movie

Orientation:

#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

#5: Superimposing with simplified surface model of EM map, EMDB-5006, Image by Jmol

#6: Superimposing with EM 3D map: EMDB-5006, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3c6r
TitleLow pH Immature Dengue Virus
DescriptorEnvelope protein
Peptide pr
KeywordsVIRUS, dengue, immature, prM, E, Capsid protein, Cleavage on pair of basic residues, Core protein, Endoplasmic reticulum, Envelope protein, Glycoprotein, Membrane, Secreted, Transmembrane, Virion, icosahedral virus, virus
AuthorsYu, I., Zhang, W., Holdway, H.A., Li, L., Kostyuchenko, V.A., Chipman, P.R., Kuhn, R.J., Rossmann, M.G., Chen, J.
DateDeposition: 2008-02-05, Release: 2008-04-22
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Sequence detailsTHE AUTHORS STATE THAT THE SEQUENCE CONFLICTS ARE DUE TO STRAIN DIFFERENCES. THE PDB ENTRY USED TO FIT INTO THE MAP IS A MODEL GENERATED FROM TWO DIFFERENT STRUCTURES.
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

#5: Superimposing with simplified surface model of EM map, EMDB-5006, Image by Jmol

#6: Superimposing with EM 3D map: EMDB-5006, Image by UCSF CHIMERA

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

EMDB-5006

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Article
Citation - primary
ArticleScience, Vol. 319, Issue 5871, Page 1834-7, Year 2008
TitleStructure of the immature dengue virus at low pH primes proteolytic maturation.
AuthorsI-Mei Yu, Wei Zhang, Heather A Holdaway, Long Li, Victor A Kostyuchenko, Paul R Chipman, Richard J Kuhn, Michael G Rossmann, Jue Chen
Department of Biological Sciences, 915 West State Street, Purdue University, West Lafayette, IN 47907-2054, USA.
KeywordsCryoelectron Microscopy, Crystallography, X-Ray, Dengue Virus (chemistry), Dimerization, E-glycoprotein, Dengue virus type 2, Endoplasmic Reticulum (virology), Furin (metabolism, 3.4.21.75), Hydrogen-Ion Concentration, Image Processing, Computer-Assisted, Membrane Fusion, Protein Conformation, Viral Envelope Proteins (chemistry), Viral Fusion Proteins (chemistry), Viral Matrix Proteins (chemistry), Virion (metabolism), trans-Golgi Network (metabolism)
LinksDOI: 10.1126/science.1153264, PubMed: 18369148
Components
ID 1 : Envelope protein
Image
DescriptionEnvelope protein
Typepolypeptide(L)
Formula weight43904.797 Da
Number of molecules3
ID1
SourceMethod: Isolated from a natural source
Organism scientific: Dengue virus type 2
Strain: Thailand/PUO-218/1980
LinksUniProt: P18356, Sequence view
ID 2 : Peptide pr
Image
DescriptionPeptide pr
Typepolypeptide(L)
Formula weight9261.574 Da
Number of molecules3
ID2
SourceMethod: Isolated from a natural source
Organism scientific: Dengue virus type 2
Strain: Thailand/PUO-218/1980
LinksUniProt: P18356, Sequence view
Sample
Assembly
Aggregation statePARTICLE
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 reconstruction
Actual pixel size2.7 A/pix
CTF correction methodBoth amplitude and phase of CTF are corrected for each boxed particle.
Magnification calibrationGrating Replica EM grid
MethodCross-correlation in real and reciprocal space for orientation determination; Fourier-Bessel method for reconstruction.
Nominal pixel size2.8 A/pix
Resolution25 A
3D fitting
Refinement SpaceREAL
Software nameEMfit
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms1422
Protein atoms1422
Download
PDB format
Allpdb3c6r.ent.gz
pdb3c6r.ent (uncompressed file)
Header onlypdb3c6r.ent.gz
mmCIF format
mmCIF3c6r.cif.gz
XML format
All3c6r.xml.gz
No-atom3c6r-noatom.xml.gz
Ext-atom3c6r-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.2 MB
movie #2
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movie #3
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movie #4
.mp4 (H.264/MPEG-4 AVC format), 2.7 MB
.webm (WebM/VP8 format), 3.6 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.9 MB
.webm (WebM/VP8 format), 5.6 MB
movie #6
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.8 MB