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

by single particle (icosahedral) reconstruction, at 9.5 A resolution

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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: Deposited structure unit, Image 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
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, Image by Jmol

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

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

#4: Deposited structure unit, Image 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 907-12, 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 weight54402.305 Da
Number of molecules3
ID1
SourceMethod: Isolated from a natural source
Genus: Flavivirus
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 weight8387.914 Da
Number of molecules3
ID2
SourceMethod: Isolated from a natural source
Genus: Flavivirus
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
Assembly
Aggregation statePARTICLE
NameDENGUE VIRUS
Entity assembly
Assembly-ID1
Virus entity
Ictvdb id00.026.0.01.013
Virus host categoryINVERTEBRATES
Virus host growth cellmosquito C6/36
Virus host speciesAedes aegypti
Virus isolateSTRAIN
Virus typeVIRION
Buffer
Name50 mM TRIS, 75 mM NaCl, 1 mM EDTA
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.6
Sample concentration20 mg/ml
Sample support
DetailsConcentration is given in PFU/ML
Vitrification
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 sourceSCHOTTKY FIELD EMISSION GUN
Accelerating voltage200 kV
Electron dose2700 e/A**2
Illumination modeFLOOD BEAM LOW DOSE
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
Detector
TypeKODAK SO163 FILM
Processing
2D projection selection
Number of particles1691
Software nameEMFIT
Single particle entity
Symmetry typeICOSAHEDRAL
3D reconstruction
CTF correction methodeach viral image was CTF corrected before reconstruction, based on the following equation: F(corr)=F(obs)/[|CTF|+wiener*(1-|CTF|)]
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
Resolution9.5 A
3D fitting
Refinement SpaceREAL
Software nameEMFIT
3D fitting list
3D Fitting ID1
PDB entry ID1SVB and 1JCH
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
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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), 2.5 MB