3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Diagram Statistics Viewer Documents
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - PDB-3iyk

Bluetongue virus structure reveals a sialic acid binding domain, amphipathic helices and a central coiled coil in the outer capsid proteins

by single particle (icosahedral) reconstruction, at 7 A resolution

Movie

Orientation:

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

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

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

#4: Depositted structure unit, Made by Jmol

#5: Superimposing with simplified surface model of EM map, EMDB-5147, Made by Jmol

#6: Superimposing with EM 3D map: EMDB-5147, Made by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3iyk
TitleBluetongue virus structure reveals a sialic acid binding domain, amphipathic helices and a central coiled coil in the outer capsid proteins
DescriptorVP5
VP2
KeywordsVIRUS, virus, Icosahedral virus
AuthorsZhang, X., Boyce, M., Bhattacharya, B., Zhang, X., Schein, S., Roy, P., Zhou, Z.H.
DateDeposition: 2010-01-25, Release: 2010-04-07
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

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

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

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

#4: Depositted structure unit, Made by Jmol

#5: Superimposing with simplified surface model of EM map, EMDB-5147, Made by Jmol

#6: Superimposing with EM 3D map: EMDB-5147, Made by UCSF CHIMERA

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

EMDB-5147
CiteFit

Cite: data citing same article

Fit: target map of fitting

Similar strucutres (beta)

Diagram

PDB-1tja

EMDB-5597
List of similar structure data about Omokage system
Article
Citation - primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 107, Issue 14, Page 6292-7, Year 2010
TitleBluetongue virus coat protein VP2 contains sialic acid-binding domains, and VP5 resembles enveloped virus fusion proteins.
AuthorsXing Zhang, Mark Boyce, Bishnupriya Bhattacharya, Xiaokang Zhang, Stan Schein, Polly Roy, Z Hong Zhou
Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095-7364, USA.
KeywordsAmino Acid Sequence, Animals, Binding Sites, Bluetongue virus (chemistry), Capsid Proteins (chemistry), Cell Line, Cricetinae, Cryoelectron Microscopy, Humans, Models, Molecular, Molecular Sequence Data, N-Acetylneuraminic Acid (chemistry, 131-48-6), Protein Multimerization, Protein Structure, Quaternary, Protein Structure, Secondary, Protein Structure, Tertiary, VP2 protein, Bluetongue virus, VP5 protein, Bluetongue virus, Viral Fusion Proteins (chemistry), Virus Replication
LinksDOI: 10.1073/pnas.0913403107, PubMed: 20332209, PMC: PMC2852009
Components
ID 1 : VP5
Image
DescriptionVP5
Typepolymer
Formula weight59071.051 Da
Number of molecules6
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:40051
Organism scientific: Bluetongue virus
LinksUniProt: C5IWW1, Sequence view
ID 2 : VP2
Image
DescriptionVP2
Typepolymer
Formula weight70500.438 Da
Number of molecules3
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:40051
Organism scientific: Bluetongue virus
LinksUniProt: C5IWV8, Sequence view
ID 3 : 2-O-METHYL-5-N-ACETYL-ALPHA-D- NEURAMINIC ACID
Image
Description2-O-METHYL-5-N-ACETYL-ALPHA-D- NEURAMINIC ACID
Typenon-polymer
Formula weight323.299 Da
Number of molecules3
SourceMethod: Obtained synthetically
Sample
Assembly
Aggregation statePARTICLE
CompositionIcosahedron
DetailsThe sample was monodisperse in ice
NameBluetongue Virus
Num components4
Entity assembly
NameBluetongue Virus
TypeVIRUS
Virus entity
EmptyNO
EnvelopedNO
Ictvdb id00.060.0.02.001
Virus host categoryVERTEBRATES
Virus host specieslivestock
Virus isolateSTRAIN
Virus typeVIRION
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
DetailsPBS
Entity assembly id1
pH8.0
Vitrification
Cryogen nameETHANE
Instrumentmanual plunger
Temp90 Kelvin
Electron Microscopy
Imaging
Microscopemodel: FEI TECNAI F20
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage200 kV
Electron dose25 e/A**2
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
Magnificationcalibrated: 79787 X, nominal: 80000 X
Csnominal: 2 mm
Detector distance0.0
Specimen holder
Specimen holdermodel: GATAN LIQUID NITROGEN, type: Gatan 626
Tilt anglemin: 0.0 degrees, max: 0.0 degrees
Temperature90 Kelvin
Detector
TypeCCD
Processing
Single particle entity
Symmetry typeICOSAHEDRAL
3D reconstruction
CTF correction methodEach particle
Methodprojection matching
Number of particles3400
Resolution7 A
Resolution methodFSC 0.143 cut-off
SoftwareFrealign IMIRS
Refine hist
Total atoms2331
Ligand atoms66
Protein atoms2265
Download
PDB format
Allpdb3iyk.ent.gz
pdb3iyk.ent (uncompressed file)
Header onlypdb3iyk.ent.gz
mmCIF format
mmCIF3iyk.cif.gz
XML format
All3iyk.xml.gz
No-atom3iyk-noatom.xml.gz
Ext-atom3iyk-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.7 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 2.7 MB
.webm (WebM/VP8 format), 3.6 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 2.6 MB
.webm (WebM/VP8 format), 3.5 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 2.6 MB
.webm (WebM/VP8 format), 3.5 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.9 MB
.webm (WebM/VP8 format), 5.9 MB
movie #6
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.1 MB