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CryoEM structure of poliovirus receptor bound to poliovirus type 2

by single particle (icosahedral) reconstruction, at 9 A resolution

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1563, Image by Jmol

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3epf
TitleCryoEM structure of poliovirus receptor bound to poliovirus type 2
DescriptorPoliovirus receptor
Protein VP1
Protein VP2
Protein VP4
Protein VP3
KeywordsVIRAL PROTEIN, CD155 structure Immunoglobulin Superfamily, poliovirus capsid jelly role, Cell adhesion, Cell membrane, Glycoprotein, Host-virus interaction, Immunoglobulin domain, Membrane, Receptor, Secreted, Transmembrane
AuthorsZhang, P., Mueller, S., Morais, M.C., Bator, C.M., Bowman, V.D., Hafenstein, S., Wimmer, E., Rossmann, M.G.
DateDeposition: 2008-09-29, Release: 2008-11-11
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1563, Image by Jmol

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EMDB-1563

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Article
Citation - primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 105, Issue 47, Page 18284-9, Year 2008
TitleCrystal structure of CD155 and electron microscopic studies of its complexes with polioviruses.
AuthorsPing Zhang, Steffen Mueller, Marc C Morais, Carol M Bator, Valorie D Bowman, Susan Hafenstein, Eckard Wimmer, Michael G Rossmann
Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054, USA.
KeywordsAmino Acid Sequence, Cell Fusion, Cryoelectron Microscopy, Crystallography, X-Ray, HeLa Cells, Humans, Models, Molecular, Molecular Sequence Data, Mutagenesis, Poliovirus (physiology), Protein Conformation, Receptors, Virus (chemistry), poliovirus receptor
LinksDOI: 10.1073/pnas.0807848105, PubMed: 19011098, PMC: PMC2587566
Components
ID 1 : Nectin-like protein 5, Necl-5
Image
DescriptionPoliovirus receptor
Typepolypeptide(L)
FragmentPoliovirus receptor CD155 D1D2
MutationN105D, N120S, N188Q, N218Q, N237S
Formula weight23330.672 Da
Number of molecules1
ID1
SourceMethod: Isolated from a genetically manipulated source
Gene: human, PVR, PVS, ID:9606, Homo sapiens
Host: ID:562, Escherichia coli

LinksUniProt: P15151, Sequence view
ID 2 : Protein VP1
Image
DescriptionProtein VP1
Typepolypeptide(L)
Formula weight30734.809 Da
Number of molecules1
ID2
SourceMethod: Isolated from a genetically manipulated source
Gene: ID:12084, Poliovirus type 2
Host: ID:562, Escherichia coli
LinksUniProt: P06210, Sequence view
ID 3 : Protein VP2
Image
DescriptionProtein VP2
Typepolypeptide(L)
Formula weight29046.006 Da
Number of molecules1
ID3
SourceMethod: Isolated from a genetically manipulated source
Gene: ID:12084, Poliovirus type 2
Host: ID:562, Escherichia coli
LinksUniProt: P06210, Sequence view
ID 4 : Protein VP4
Image
DescriptionProtein VP4
Typepolypeptide(L)
Formula weight7347.032 Da
Number of molecules1
ID4
SourceMethod: Isolated from a genetically manipulated source
Gene: ID:12084, Poliovirus type 2
Host: ID:562, Escherichia coli
LinksUniProt: P06210, Sequence view
ID 5 : Protein VP3
Image
DescriptionProtein VP3
Typepolypeptide(L)
Formula weight26115.982 Da
Number of molecules1
ID5
SourceMethod: Isolated from a genetically manipulated source
Gene: ID:12084, Poliovirus type 2
Host: ID:562, Escherichia coli
LinksUniProt: P06210, Sequence view
ID 6 : 1[2-CHLORO-4-METHOXY-PHENYL-OXYMETHYL]-4-[2,6-DICHLORO-PHENYL-OXYMETHYL]-BENZENE
Image
Description1[2-CHLORO-4-METHOXY-PHENYL-OXYMETHYL]-4-[2,6-DICHLORO-PHENYL-OXYMETHYL]-BENZENE
Typenon-polymer
Formula weight423.723 Da
Number of molecules1
ID6
SourceMethod: Obtained synthetically
ID 7 : MYRISTIC ACID
Image
DescriptionMYRISTIC ACID
Typenon-polymer
Formula weight228.374 Da
Number of molecules1
ID7
SourceMethod: Obtained synthetically
ID 8 : water
Image
Descriptionwater
Typewater
Formula weight18.015 Da
Number of molecules271
ID8
SourceMethod: Isolated from a natural source
Sample
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Processing
2D projection selection
Software nameEMfit
3D reconstruction
Actual pixel size2.66 A/pix
Nominal pixel size2.69 A/pix
Resolution9.0 A
3D fitting
Refinement SpaceREAL
Software nameEMfit
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Solvent atoms271
Total atoms8461
Ligand atoms38
Protein atoms8152
Download
PDB format
Allpdb3epf.ent.gz
pdb3epf.ent (uncompressed file)
Header onlypdb3epf.ent.gz
mmCIF format
mmCIF3epf.cif.gz
XML format
All3epf.xml.gz
No-atom3epf-noatom.xml.gz
Ext-atom3epf-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.5 MB
.webm (WebM/VP8 format), 3.4 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.1 MB