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Pseudo-atomic structure of the E2-E1 protein shell in Sindbis virus

by single particle (icosahedral) reconstruction, at 9 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: Deposited structure unit, Image by Jmol

#5: Superimposing with simplified surface model of EM map, EMDB-1121, Image by Jmol

#6: Superimposing with EM 3D map: EMDB-1121, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3muw
TitlePseudo-atomic structure of the E2-E1 protein shell in Sindbis virus
DescriptorStructural polyprotein (E.C.3.4.21.-)
KeywordsVIRUS, icosahedral protein shell, icosahedral virus
AuthorsLi, L., Jose, J., Xiang, Y., Kuhn, R.J., Rossmann, M.G.
DateDeposition: 2010-05-03, Release: 2010-11-24
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

#5: Superimposing with simplified surface model of EM map, EMDB-1121, Image by Jmol

#6: Superimposing with EM 3D map: EMDB-1121, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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Article
Citation - primary
ArticleNature, Vol. 468, Issue 7324, Page 705-8, Year 2010
TitleStructural changes of envelope proteins during alphavirus fusion.
AuthorsLong Li, Joyce Jose, Ye Xiang, Richard J Kuhn, Michael G Rossmann
Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, Indiana 47907-2054, USA.
KeywordsAnimals, Cell Line, Cryoelectron Microscopy, Crystallography, X-Ray, Drosophila melanogaster, Endosomes (metabolism), Hydrogen-Ion Concentration, Hydrophobic and Hydrophilic Interactions, Membrane Fusion, Membrane Glycoproteins (chemistry), Models, Molecular, Protein Multimerization, Protein Structure, Quaternary, Protein Structure, Tertiary, Receptors, Virus (metabolism), Sindbis Virus (chemistry), Viral Envelope Proteins (chemistry), Viral Fusion Proteins (chemistry), Virion (chemistry), Virus Internalization, glycoprotein E1, Sindbis virus, glycoprotein E2, Sindbis virus
LinksDOI: 10.1038/nature09546, PubMed: 21124457, PMC: PMC3057476
Components
ID 1 : p130, Capsid protein, Coat protein, C, p62, E3/E2, E3 protein, Spike glycoprotein E3, E2 envelope glycoprotein, Spike glycoprotein E2, 6K protein, E1 envelope glycoprotein, Spike glycoprotein E1
Image
DescriptionStructural polyprotein
Typepolypeptide(L)
Formula weight41312.125 Da
Number of molecules4
ID1
Ec3.4.21.-
SourceMethod: Isolated from a natural source
Common name: SINV
NCBI taxonomy: ID:11034
Organism scientific: Sindbis virus
Strain: Toto64
LinksUniProt: P03316, Sequence view
ID 2 : p130, Capsid protein, Coat protein, C, p62, E3/E2, E3 protein, Spike glycoprotein E3, E2 envelope glycoprotein, Spike glycoprotein E2, 6K protein, E1 envelope glycoprotein, Spike glycoprotein E1
Image
DescriptionStructural polyprotein
Typepolypeptide(L)
Formula weight38509.012 Da
Number of molecules4
ID2
Ec3.4.21.-
SourceMethod: Isolated from a natural source
Common name: SINV
NCBI taxonomy: ID:11034
Organism scientific: Sindbis virus
Strain: Toto64
LinksUniProt: P03316, Sequence view
Sample
Assembly
Aggregation statePARTICLE
NameSindbis virus
Entity assembly
Assembly-ID1
NameE2-E1 protein shell of Sindbis virus
Virus entity
Ictvdb idToto64
Virus host categoryVERTEBRATES
Virus host growth cellBHK cell
Virus host specieshomo sapiens
Virus isolateSTRAIN
Virus typeVirion
Buffer
NameTNE buffer
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.5
Sample concentration5 mg/ml
Sample support
DetailsThis grid plus sample was kept at 100 K
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI/PHILIPS CM200T
Date2000-06-21
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage200 kV
Electron dose18 e/A**2
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 39220 X, Nominal: 38000 X
CsNominal: 2.0 mm
Nominal defocusMax: 2580 nm, Min: 1100 nm
Specimen holder
Tilt angleMin: 0 degrees, Max: 0 degrees
Detector
TypeKodak SO163 film
Processing
2D projection selection
Number of particles7085
Software nameEMfit
Single particle entity
Symmetry typeICOSAHEDRAL
3D reconstruction
CTF correction methodCTF correction of each particle.
Methodmodel-based common lines
Resolution9.0 A
3D fitting
Refinement Protocolrigid body
Refinement SpaceREAL
Software nameEMfit
Target criteriasumf
3D fitting list
3D Fitting ID1
PDB entry ID3MUU
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms2468
Protein atoms2468
Download
PDB format
Allpdb3muw.ent.gz
pdb3muw.ent (uncompressed file)
Header onlypdb3muw.ent.gz
mmCIF format
mmCIF3muw.cif.gz
XML format
All3muw.xml.gz
No-atom3muw-noatom.xml.gz
Ext-atom3muw-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 4.3 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 3.2 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 3 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 2.9 MB
.webm (WebM/VP8 format), 2.9 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.9 MB
.webm (WebM/VP8 format), 3.7 MB
movie #6
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.2 MB