PDB-3epf: CryoEM structure of poliovirus receptor bound to poliov...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 3epf
Title	CryoEM structure of poliovirus receptor bound to poliovirus type 2
Descriptor	Poliovirus receptor Protein VP1 Protein VP2 Protein VP4 Protein VP3
Keywords	VIRAL PROTEIN, CD155 structure Immunoglobulin Superfamily, poliovirus capsid jelly role, Cell adhesion, Cell membrane, Glycoprotein, Host-virus interaction, Immunoglobulin domain, Membrane, Receptor, Secreted, Transmembrane
Authors	Zhang, P., Mueller, S., Morais, M.C., Bator, C.M., Bowman, V.D., Hafenstein, S., Wimmer, E., Rossmann, M.G.
Date	Deposition: 2008-09-29, Release: 2008-11-11
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol #2: Superimposing with simplified surface model of EM map, EMDB-1563, Made by Jmol
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1563 CiteFit EMDB-1562 Cite EMDB-1570 Cite PDB-3epc Cite PDB-3epd Cite PDB-3uro Cite PDB-3eow Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-3epd PDB-3epc PDB-3iyp PDB-3iz0 List of similar structure data about Omokage system

Article
Citation - primary
Article	Proc. Natl. Acad. Sci. U.S.A., Vol. 105, Issue 47, Page 18284-9, Year 2008
Title	Crystal structure of CD155 and electron microscopic studies of its complexes with polioviruses.
Authors	Ping 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.
Keywords	Amino 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
Links	DOI: 10.1073/pnas.0807848105, PubMed: 19011098, PMC: PMC2587566

Components
ID 1 : Nectin-like protein 5, Necl-5
Image
Description	Poliovirus receptor
Type	polymer
Fragment	Poliovirus receptor CD155 D1D2
Mutation	N105D, N120S, N188Q, N218Q, N237S
Formula weight	23330.672 Da
Number of molecules	1
Source	Method: Isolated from a genetically manipulated source Gene: human, PVR, PVS, ID:9606, Homo sapiens Host: ID:562, Escherichia coli
Links	UniProt: P15151, Sequence view
ID 2 : Protein VP1
Image
Description	Protein VP1
Type	polymer
Formula weight	30734.809 Da
Number of molecules	1
Source	Method: Isolated from a genetically manipulated source Gene: ID:12084, Poliovirus type 2 Host: ID:562, Escherichia coli
Links	UniProt: P06210, Sequence view
ID 3 : Protein VP2
Image
Description	Protein VP2
Type	polymer
Formula weight	29046.006 Da
Number of molecules	1
Source	Method: Isolated from a genetically manipulated source Gene: ID:12084, Poliovirus type 2 Host: ID:562, Escherichia coli
Links	UniProt: P06210, Sequence view
ID 4 : Protein VP4
Image
Description	Protein VP4
Type	polymer
Formula weight	7347.032 Da
Number of molecules	1
Source	Method: Isolated from a genetically manipulated source Gene: ID:12084, Poliovirus type 2 Host: ID:562, Escherichia coli
Links	UniProt: P06210, Sequence view
ID 5 : Protein VP3
Image
Description	Protein VP3
Type	polymer
Formula weight	26115.982 Da
Number of molecules	1
Source	Method: Isolated from a genetically manipulated source Gene: ID:12084, Poliovirus type 2 Host: ID:562, Escherichia coli
Links	UniProt: P06210, Sequence view
ID 6 : 1[2-CHLORO-4-METHOXY-PHENYL-OXYMETHYL]-4-[2,6-DICHLORO-PHENYL-OXYMETHYL]-BENZENE
Image
Description	1[2-CHLORO-4-METHOXY-PHENYL-OXYMETHYL]-4-[2,6-DICHLORO-PHENYL-OXYMETHYL]-BENZENE
Type	non-polymer
Formula weight	423.723 Da
Number of molecules	1
Source	Method: Obtained synthetically
ID 7 : MYRISTIC ACID
Image
Description	MYRISTIC ACID
Type	non-polymer
Formula weight	228.374 Da
Number of molecules	1
Source	Method: Obtained synthetically
ID 8 : water
Image
Description	water
Type	water
Formula weight	18.015 Da
Number of molecules	271
Source	Method: Isolated from a natural source

Sample

Electron Microscopy

Processing
2D projection selection
Software name	EMfit
3D reconstruction
Actual pixel size	2.66 A/pix
Nominal pixel size	2.69 A/pix
Resolution	9.0 A
3D fitting
Refinement Space	REAL
Software name	EMfit
Refine hist
Solvent atoms	271
Total atoms	8461
Ligand atoms	38
Protein atoms	8152