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Complex Organization of Dengue Virus Membrane Proteins as Revealed by 9.5 Angstrom Cryo-EM reconstruction

by single particle reconstruction, at 9.5 A resolution

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

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

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

#4: Deposited structure unit, Imaged by Jmol

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 1p58
TitleComplex Organization of Dengue Virus Membrane Proteins as Revealed by 9.5 Angstrom Cryo-EM reconstruction
DescriptorMajor envelope protein E/Envelope glycoprotein M
KeywordsVIRUS, FLAVIVIRUS, FLAVIVIRIDAE, DENGUE VIRUS, GLYCOPROTEIN E FROM TICK-BORNE ENCEPHALITIS VIRUS, MEMBRANE PROTEIN M, CRYO-EM, Icosahedral virus, Virus
AuthorsZhang, W., Chipman, P.R., Corver, J., Johnson, P.R., Zhang, Y., Mukhopadhyay, S., Baker, T.S., Strauss, J.H., Rossmann, M.G., Kuhn, R.J.
DateDeposition: 2003-04-25, Release: 2003-11-04
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, Imaged by Jmol

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

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

#4: Deposited structure unit, Imaged by Jmol

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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Article
Citation - primary
ArticleNat. Struct. Biol., Vol. 10, Issue 11, Page 907-912, Year 2003
TitleVisualization of membrane protein domains by cryo-electron microscopy of dengue virus.
AuthorsWei Zhang, Paul R Chipman, Jeroen Corver, Peter R Johnson, Ying Zhang, Suchetana Mukhopadhyay, Timothy S Baker, James H Strauss, Michael G Rossmann, Richard J Kuhn
Department of Biological Sciences, Lilly Hall, 915 W. State Street, Purdue University, West Lafayette, Indiana 47907, USA.
KeywordsCryoelectron Microscopy, Dengue Virus (metabolism), Nucleocapsid (metabolism), Protein Structure, Secondary, Protein Structure, Tertiary, Viral Matrix Proteins (metabolism)
LinksPubMed: 14528291, DOI: 10.1038/nsb990, PMC: PMC4148076
Citation - 1
ArticleCell(Cambridge,Mass.), Vol. 108, Page: 717 - 725, Year: 2002,
TitleStructure of Dengue Virus: Implications for Flaviviruses Organization, Maturation and Fusion
AuthorsKuhn, R.J., Zhang, W., Rossmann, M.G., Pletnev, S.V., Corver, J., Lenches, E., Jones, C.T., Mukhopadhyay, S., Chipman, P.R., Strauss, E.G., Baker, T.S., Strauss, J.H.
Citation - 2
ArticleNature, Vol. 375, Page: 291 - 298, Year: 1995,
TitleThe envelope glycoprotein from tick-borne encephalitis virus at 2 A resolution
AuthorsRey, F.A., Heinz, F.X., Mandl, C., Kunz, C., Harrison, S.C.
Citation - 3
ArticleNature, Vol. 375, Page: 275 - 276, Year: 1995,
TitleVirology. When it's better to lie low.
AuthorsKuhn, R.J., Rossmann, M.G.
Citation - 4
ArticleMicrobiol.Mol.Biol.Rev., Vol. 63, Page: 862 - 922, Year: 1999,
TitleAdding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs
AuthorsBaker, T.S., Olson, N.H., Fuller, S.D.
Components
ID 1 : Major envelope protein E
Image
DescriptionMajor envelope protein E
Typepolypeptide(L)
Formula weight54401.758 Da
Number of molecules3
ID1
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Flavivirus
Alt source flag: sample
NCBI taxonomy: ID:11066
Organism scientific: Dengue virus 2 Puerto Rico/PR159-S1/1969
Species: Dengue virus
Strain: PR159/S1
LinksUniProt: P12823, Sequence view
ID 2 : Envelope protein M
Image
DescriptionEnvelope protein M
Typepolypeptide(L)
Formula weight8387.841 Da
Number of molecules3
ID2
SourceMethod: Isolated from a natural source
Src id: 1
Genus: Flavivirus
Alt source flag: sample
NCBI taxonomy: ID:11066
Organism scientific: Dengue virus 2 Puerto Rico/PR159-S1/1969
Species: Dengue virus
Strain: PR159/S1
LinksUniProt: P12823, Sequence view
Sample
Entity assembly
NameDENGUE VIRUS
TypeVIRUS
Virus entity
Virus host categoryINVERTEBRATES
Virus isolateSTRAIN
Virus typeVIRION
Buffer
Specimen id1
Details50 mM TRIS, 75 mM NaCl, 1 mM EDTA
Name50 mM TRIS, 75 mM NaCl, 1 mM EDTA
PH7.6
Experiment
Aggregation statePARTICLE
Reconstruction methodSINGLE PARTICLE
Sample support
Specimen id1
DetailsConcentration is given in PFU/ML
Vitrification
Specimen id1
DetailsSAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI/PHILIPS CM200T
Date2000-06-27
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage200 kV
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationNominal: 50000 X
CsNominal: 2.0 mm
Nominal defocusMax: 4800.0 nm, Min: 800.0 nm
Specimen holder
Tilt angleMin: 0.0 degrees, Max: 0.0 degrees
Temperature87 Kelvin
Image scans
Image recording id1
Processing
Single particle entity
Image processing id1
Point symmetryI
3D reconstruction
Image processing id1
DetailsTHE RECONSTRUCTION WAS COMPUTED FROM 1691 DENGUE VIRUS IMAGES THAT WERE SELECTED FROM 78 MICROGRAPHS. ORIENTATIONS WERE DETERMINED BY THE MODEL-BASED POLAR-FOURIER TRANSFORM METHOD (BAKER AND CHENG, 1996, J.STRUC.BIOL. 116,120-130) AND REFINED BY THE MODEL-BASED FOURIER TRANSFORM REFINEMENT PROCEDURE(http://bond.cs.ucf.edu/ComputationalBiology/Projects/POR/Home.html).
MethodFOURIER-BESSEL METHOD
Nominal pixel size2.8 A/pix
Number of particles1691
Resolution9.5 A
Symmetry typePOINT
3D fitting
Refinement SpaceREAL
3D fitting list
3D Fitting ID1
PDB entry ID1SVB
3D fitting list
3D Fitting ID1
PDB entry ID1JCH
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms1635
Protein atoms1635
Download
PDB format
Allpdb1p58.ent.gz
pdb1p58.ent (uncompressed file)
Header onlypdb1p58.ent.gz
mmCIF format
mmCIF1p58.cif.gz
XML format
All1p58.xml.gz
No-atom1p58-noatom.xml.gz
Ext-atom1p58-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.9 MB
.webm (WebM/VP8 format), 4.3 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 6 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 7.6 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 2.7 MB
.webm (WebM/VP8 format), 2.5 MB