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COMPLEX OF ECHOVIRUS TYPE 12 WITH DOMAINS 3 AND 4 OF ITS RECEPTOR DECAY ACCELERATING FACTOR (CD55) BY CRYO ELECTRON MICROSCOPY AT 16 A

by single particle (icosahedral) reconstruction, at 16 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

#5: Superimposing with simplified surface model of EM map, EMDB-1057, Image by Jmol

#6: Superimposing with simplified surface model of EM map, EMDB-1058, Image by Jmol

#7: Superimposing with EM 3D map: EMDB-1057, Image by UCSF CHIMERA

#8: Superimposing with EM 3D map: EMDB-1058, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 1upn
TitleCOMPLEX OF ECHOVIRUS TYPE 12 WITH DOMAINS 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, COMPLEX (VIRUS COAT-IMMUNE PROTEIN), ECHOVIRUS, PICORNAVIRUS, CD55, DAF, VIRUS-RECEPTOR COMPLEX, ICOSAHEDRAL VIRUS
AuthorsBhella, D., Goodfellow, I.G., Roversi, P., Pettigrew, D., Chaudry, Y., Evans, D.J., Lea, S.M.
DateDeposition: 2003-10-08, Release: 2004-01-07
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Sequence detailsTHE SEQUENCE OF THE ECHOVIRUS CAPSID PROTEINS IS FROM EV11 BUT THE EM DENSITY INTO WHICH THE STRUCTURE WAS FITTED IS THAT OF EV12
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-1057, Image by Jmol

#6: Superimposing with simplified surface model of EM map, EMDB-1058, Image by Jmol

#7: Superimposing with EM 3D map: EMDB-1057, Image by UCSF CHIMERA

#8: Superimposing with EM 3D map: EMDB-1058, Image by UCSF CHIMERA

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

EMDB-1057

CiteFit

EMDB-1058

CiteFit

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Fit: target map of fitting

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Article
Citation - primary
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 weight32786.949 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:12078
Organism scientific: HUMAN ECHOVIRUS 11
Strain: GREGORY
LinksUniProt: Q8JKE8, Sequence view
ID 2 : ECHOVIRUS 11 COAT PROTEIN VP2
Image
DescriptionECHOVIRUS 11 COAT PROTEIN VP2
Typepolypeptide(L)
Formula weight29048.713 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
NCBI taxonomy: ID:12078
Organism scientific: HUMAN ECHOVIRUS 11
Strain: GREGORY
LinksUniProt: Q8JKE8, 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: Q8JKE8, Sequence view
ID 4 : ECHOVIRUS 11 COAT PROTEIN VP4
Image
DescriptionECHOVIRUS 11 COAT PROTEIN VP4
Typepolypeptide(L)
Formula weight7509.366 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: Q8JKE8, Sequence view
ID 5 : CD55
Image
DescriptionCOMPLEMENT DECAY-ACCELERATING FACTOR
Typepolypeptide(L)
Formula weight14094.814 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
NameECHOVIRUS TYPE 12
Buffer
NameAMMONIUM MOLYBDATE
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.4
Sample concentration0.2 mg/ml
Sample support
DetailsHOLEY CARBON
Vitrification
DetailsLIQUID ETHANE
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: JEOL 1200 EX II
Date2002-07-15
DetailsPARTICLES SELECTED WITH X3D
Electron gun
Electron sourceLAB6
Accelerating voltage120 kV
Illumination modeLOW DOSE
Lens
MagnificationCalibrated: 29200 X, Nominal: 30000 X
CsNominal: 3.4 mm
Nominal defocusMax: 2000 nm, Min: 300 nm
Specimen holder
Temperature108 Kelvin
Detector
TypeKODAK SO-163 FILM
Image scans
Number digital images16
Processing
2D projection selection
Software nameMRC
Single particle entity
Symmetry typeICOSAHEDRAL
3D reconstruction
DetailsMAP BROUGHT TO P23 CRYSTAL WITH UNIT CELL DIMENSIONS OF 599.375 599.375 599.375 90.00 90.00 90.00. MODEL FOR EV11 DOCKED ONTO EV12 EM DENSITY. 0.5 A GAP BETWEEN CD55 DOMAIN 3 AND DOMAIN 4 WAS INTRODUCED BY RIGID-BODY REFINEMENT OF DOMAIN 4 KEEPING 3 FIXED
MethodPOLAR FOURIER TRANSFORM
3D fitting
Refinement ProtocolX-RAY
Refinement SpaceREAL
Target criteriaCORRELATION COEFFICIENTS
3D fitting list
3D Fitting ID1
Refine
Refine idELECTRON MICROSCOPY
Ls d res high16.00 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high16.00
Total atoms7463
Protein atoms7463
Download
PDB format
Allpdb1upn.ent.gz
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Header onlypdb1upn.ent.gz
mmCIF format
mmCIF1upn.cif.gz
XML format
All1upn.xml.gz
No-atom1upn-noatom.xml.gz
Ext-atom1upn-extatom.xml.gz
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