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Complex Of Echovirus Type 12 With Domains 1, 2, 3 and 4 Of Its Receptor Decay Accelerating Factor (Cd55) By Cryo Electron Microscopy At 16 A

by single particle (icosahedral) reconstruction, at 14 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: Depositted structure unit, Image by Jmol

#5: Superimposing with simplified surface model of EM map, EMDB-1182, Image by Jmol

#6: Superimposing with simplified surface model of EM map, EMDB-1183, Image by Jmol

#7: Superimposing with EM 3D map: EMDB-1182, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 2c8i
TitleComplex Of Echovirus Type 12 With Domains 1, 2, 3 and 4 Of Its Receptor Decay Accelerating Factor (Cd55) By Cryo Electron Microscopy At 16 A
DescriptorECHOVIRUS 11 COAT PROTEIN VP1
ECHOVIRUS 11 COAT PROTEIN VP2
ECHOVIRUS 11 COAT PROTEIN VP3
ECHOVIRUS 11 COAT PROTEIN VP4
COMPLEMENT DECAY-ACCELERATING FACTOR
KeywordsVIRUS/RECEPTOR, PICORNAVIRUS, DAF, VIRUS-RECEPTOR COMPLEX, ANTIGEN, BLOOD GROUP ANTIGEN, COMPLEMENT PATHWAY, GPI-ANCHOR, IMMUNE RESPONSE, INNATE IMMUNITY, LIPOPROTEIN, PLASMA, SUSHI
AuthorsPettigrew, D.M., Williams, D.T., Kerrigan, D., Evans, D.J., Lea, S.M., Bhella, D.
DateDeposition: 2005-12-05, Release: 2006-01-17
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, 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-1182, Image by Jmol

#6: Superimposing with simplified surface model of EM map, EMDB-1183, Image by Jmol

#7: Superimposing with EM 3D map: EMDB-1182, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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EMDB-1182

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EMDB-1183

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Article
Citation - primary
ArticleJ. Biol. Chem., Vol. 281, Issue 8, Page 5169-77, Year 2006
TitleStructural and functional insights into the interaction of echoviruses and decay-accelerating factor.
AuthorsDavid M Pettigrew, David T Williams, David Kerrigan, David J Evans, Susan M Lea, David Bhella
Medical Research Council Virology Unit, Institute of Biomedical and Life Sciences, University of Glasgow, Scotland, United Kingdom.
KeywordsAntigens, CD55 (metabolism), Capsid Proteins (chemistry), Cell Line, Tumor, Cryoelectron Microscopy, Databases, Protein, Electrons, Enterovirus B, Human (chemistry), Humans, Image Processing, Computer-Assisted, Microscopy, Electron, Microscopy, Electron, Transmission, Microscopy, Video, Models, Molecular, Pichia, Protein Binding, Protein Conformation, Receptors, Virus (chemistry), Recombinant Proteins (chemistry), Rhabdomyosarcoma (metabolism), Stereoisomerism, Surface Plasmon Resonance, VP2 protein, Echovirus
LinksDOI: 10.1074/jbc.M510362200, PubMed: 16272562
Citation - 1
ArticleJ. Biol. Chem., Vol. 279, Issue 9, Page 8325-32, Year 2004
TitleThe structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55).
AuthorsDavid Bhella, Ian G Goodfellow, Pietro Roversi, David Pettigrew, Yasmin Chaudhry, David J Evans, Susan M Lea
Medical Research Council Virology Unit, Church Street, Glasgow, G11 5JR, United Kingdom.
KeywordsAntigens, CD55 (metabolism), Binding Sites, Computer Simulation, Crystallization, Crystallography, X-Ray, Enterovirus B, Human (metabolism), Image Processing, Computer-Assisted, Microscopy, Electron, Models, Molecular
LinksPubMed: 14634014, DOI: 10.1074/jbc.M311334200
Components
ID 1 : ECHOVIRUS 11 COAT PROTEIN VP1
Image
DescriptionECHOVIRUS 11 COAT PROTEIN VP1
Typepolypeptide(L)
Formula weight32447.619 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:12078
Organism scientific: HUMAN ECHOVIRUS 11
Strain: GREGORY
LinksUniProt: P29813, Sequence view
ID 2 : ECHOVIRUS 11 COAT PROTEIN VP2
Image
DescriptionECHOVIRUS 11 COAT PROTEIN VP2
Typepolypeptide(L)
Formula weight27996.631 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:12078
Organism scientific: HUMAN ECHOVIRUS 11
Strain: GREGORY
LinksUniProt: P29813, Sequence view
ID 3 : ECHOVIRUS 11 COAT PROTEIN VP3
Image
DescriptionECHOVIRUS 11 COAT PROTEIN VP3
Typepolypeptide(L)
Formula weight25897.541 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:12078
Organism scientific: HUMAN ECHOVIRUS 11
Strain: GREGORY
LinksUniProt: P29813, Sequence view
ID 4 : ECHOVIRUS 11 COAT PROTEIN VP4
Image
DescriptionECHOVIRUS 11 COAT PROTEIN VP4
Typepolypeptide(L)
Formula weight6620.352 Da
Number of molecules1
ID4
DetailsSTRUCTURE OF ECHOVIRUS TYPE 11 FITTED INTO CRYO-EM ELECTRON DENSITY FOR ECHOVIRUS TYPE 12. THE EM DENSITY HAS BEEN DEPOSITED IN THE EMDB, WITH ACCESSION CODE 1057
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:12078
Organism scientific: HUMAN ECHOVIRUS 11
Strain: GREGORY
LinksUniProt: P29813, Sequence view
ID 5 : CD55
Image
DescriptionCOMPLEMENT DECAY-ACCELERATING FACTOR
Typepolypeptide(L)
Formula weight35034.414 Da
Number of molecules1
ID5
SourceMethod: Isolated from a genetically manipulated source
Gene: HUMAN, ID:9606, HOMO SAPIENS
Host: ID:562, ESCHERICHIA COLI

LinksUniProt: P08174, Sequence view
Sample
Assembly
Aggregation statePARTICLE
DetailsCRYO-NEGATIVE STAIN IMAGES. 96 FOCAL PAIRS.
NameECHOVIRUS TYPE 12 BOUND TO DECAY ACCELERATING FACTOR
Buffer
NamePHOSPHATE BUFFERED SALINE
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.4
Sample concentration0.2 mg/ml
Sample support
DetailsHOLEY CARBON
Vitrification
DetailsSTAINED WITH AMMONIUM MOLYBDATE PH 7.2. VITRIFIED IN LIQUID ETHANE (CRYO-NEGATIVE STAIN)
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
Date2004-09-01
Electron gun
Electron sourceLAB6
Accelerating voltage120 kV
Illumination modeLOW DOSE
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 29100 X, Nominal: 30000 X
CsNominal: 3.4 mm
Nominal defocusMax: 2800 nm, Min: 600 nm
Specimen holder
Tilt angleMin: 0 degrees, Max: 0 degrees
Temperature100 Kelvin
Detector
TypeKODAK SO163
Image scans
Number digital images192
Processing
2D projection selection
Number of particles1742
Software nameEM3DR2, PFT2
Single particle entity
Symmetry typeICOSAHEDRAL
3D reconstruction
Actual pixel size2.18 A/pix
CTF correction methodDEFOCUS PAIR IMAGES OF INDIVIDUAL PARTICLES
DetailsTHE SEQUENCE OF THE ECHOVIRUS CAPSID PROTEINS IS FROM EV11 BUT THE EM DENSITY INTO WHICH THE STRUCTURE WAS FITTED IS THAT OF EV12
MethodPOLAR FOURIER TRANSFORM METHOD
Nominal pixel size2.18 A/pix
Resolution14 A
3D fitting
MethodLOCAL CORRELATION
Refinement ProtocolLOCAL CORRELATION
Refinement SpaceREAL
Target criteriaOPTIMAL CORRELATION
3D fitting list
3D Fitting ID1
PDB entry ID1H8T
Refine
Refine idELECTRON MICROSCOPY
Ls d res high14.00 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high14.00
Total atoms1091
Protein atoms1091
Download
PDB format
Allpdb2c8i.ent.gz
pdb2c8i.ent (uncompressed file)
Header onlypdb2c8i.ent.gz
mmCIF format
mmCIF2c8i.cif.gz
XML format
All2c8i.xml.gz
No-atom2c8i-noatom.xml.gz
Ext-atom2c8i-extatom.xml.gz
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