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structural model of human decay-accelerating factor bound to echovirus 7 from cryo-electron microscopy

by single particle (icosahedral) reconstruction, at 16 A resolution

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#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

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 1m11
Titlestructural model of human decay-accelerating factor bound to echovirus 7 from cryo-electron microscopy
Descriptordecay-accelerating factor/coat protein VP1/coat protein VP2/coat protein VP3
KeywordsVirus/Receptor, decay-accelerating factor, SCR, Icosahedral virus, Virus-Receptor COMPLEX
AuthorsHe, Y., Lin, F., Chipman, P.R., Bator, C.M., Baker, T.S., Shoham, M., Kuhn, R.J., Medof, M.E., Rossmann, M.G.
DateDeposition: 2002-06-17, Release: 2002-08-28
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

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

PDB-1cov
 

PDB-1ev1
 

PDB-1g40
 

PDB-1upn
 

PDB-2c8i
 
Similar strucutres (beta)

Diagram

PDB-3j2k

PDB-3eq3

EMDB-1788

EMDB-2181
List of similar structure data about Omokage system
Article
Citation - primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 99, Issue 16, Page 10325-9, Year 2002
TitleStructure of decay-accelerating factor bound to echovirus 7: a virus-receptor complex.
AuthorsYongning He, Feng Lin, Paul R Chipman, Carol M Bator, Timothy S Baker, Menachem Shoham, Richard J Kuhn, M Edward Medof, Michael G Rossmann
Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA.
KeywordsAntigens, CD55 (chemistry), Cryoelectron Microscopy (methods), Enterovirus B, Human (chemistry), Humans, Models, Molecular, Protein Structure, Tertiary, Receptors, Virus (chemistry)
LinksPubMed: 12119400, DOI: 10.1073/pnas.152161599, PMC: PMC124913
Components
ID 1 : decay-accelerating factor
Image
Descriptiondecay-accelerating factor
Typepolymer
Fragmentfour SCR domains 1 to 4
Formula weight27017.459 Da
Number of molecules1
SourceMethod: Isolated from a genetically manipulated source
Gene: human, Homo, ID:9606, Homo sapiens
Host: Pichia, ID:4922, Pichia pastoris
LinksUniProt: P08174, Sequence view
ID 2 : COAT PROTEIN VP1
Image
DescriptionCOAT PROTEIN VP1
Typepolymer
Formula weight31682.660 Da
Number of molecules1
SourceMethod: Isolated from a genetically manipulated source
Gene: Enterovirus, Human enterovirus B, ID:46018, Human echovirus 7
Host: human, Homo, RD, ID:9606, Homo sapiens, muscle
Description: RHABDOMYOSARCOMA CELL (RD);
LinksUniProt: Q914E0, Sequence view
ID 3 : COAT PROTEIN VP2
Image
DescriptionCOAT PROTEIN VP2
Typepolymer
Formula weight28443.307 Da
Number of molecules1
SourceMethod: Isolated from a genetically manipulated source
Gene: Enterovirus, Human enterovirus B, ID:46018, Human echovirus 7
Host: human, Homo, RD, ID:9606, Homo sapiens, muscle
Description: RHABDOMYOSARCOMA CELL (RD);
LinksUniProt: Q914E0, Sequence view
ID 4 : COAT PROTEIN VP3
Image
DescriptionCOAT PROTEIN VP3
Typepolymer
Formula weight26264.133 Da
Number of molecules1
SourceMethod: Isolated from a genetically manipulated source
Gene: Enterovirus, Human enterovirus B, ID:46018, Human echovirus 7
Host: human, Homo, RD, ID:9606, Homo sapiens, muscle
Description: RHABDOMYOSARCOMA CELL (RD)
LinksUniProt: Q914E0, Sequence view
Sample
Assembly
Aggregation statePARTICLE
DetailsThis structure is modeled based on cryo-EM density at 16A resolution.
Namehuman decay-accelerating factor, HUMAN ECHOVIRUS 7 COAT PROTEINS
Buffer
Nametris buffer pH7.5
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.5
Sample concentration8.0 mg/ml
Vitrification
DetailsSAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE WITH A GATAN 626 CRYOTRANSFER HOLDER
Electron Microscopy
Imaging
Microscopemodel: FEI/PHILIPS CM300FEG/T
Date2001-09-10
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Electron dose1660 e/A**2
Lens
ModeBRIGHT FIELD
Magnificationnominal: 45000 X
Nominal defocusmax: 4200 nm, min: 1800 nm
Specimen holder
Temperature120 Kelvin
Processing
2D projection selection
Software nameEMFIT
Single particle entity
Symmetry typeICOSAHEDRAL
3D reconstruction
CTF correction methodCTF correction of each micrograph
DetailsThe echovirus 7 structure is unknown, the model used here is from coxsackievirus B3 (1COV) and echovirus 1 (1EV1).The DAF receptor model is from 1g40. Only CA coordinates are presented in the entry.
MethodPFT
Nominal pixel size3.11 A/pix
Resolution16.0 A
3D fitting
Refinement SpaceREAL
Software nameEMFIT
Refine
Ls d res high16.0 A
ID1
Refine hist
D res high16.0
Total atoms1013
Protein atoms1013
Download
PDB format
Allpdb1m11.ent.gz
pdb1m11.ent (uncompressed file)
Header onlypdb1m11.ent.gz
mmCIF format
mmCIF1m11.cif.gz
XML format
All1m11.xml.gz
No-atom1m11-noatom.xml.gz
Ext-atom1m11-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.1 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 4 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 2.7 MB
.webm (WebM/VP8 format), 3.6 MB