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PDBsum entry 3epf

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protein ligands Protein-protein interface(s) links
Viral protein PDB id
3epf
Jmol
Contents
Protein chains
213 a.a. *
272 a.a. *
262 a.a. *
68 a.a. *
235 a.a. *
Ligands
SC4
MYR
Waters ×271
* Residue conservation analysis
PDB id:
3epf
Name: Viral protein
Title: Cryoem structure of poliovirus receptor bound to poliovirus type 2
Structure: Poliovirus receptor. Chain: r. Fragment: poliovirus receptor cd155 d1d2. Synonym: nectin-like protein 5, necl-5. Engineered: yes. Mutation: yes. Protein vp1. Chain: 1. Engineered: yes.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: pvr, pvs. Expressed in: escherichia coli. Expression_system_taxid: 562. Poliovirus type 2. Organism_taxid: 12084. Expression_system_taxid: 562
Authors: P.Zhang,S.Mueller,M.C.Morais,C.M.Bator,V.D.Bowman, S.Hafenstein,E.Wimmer,M.G.Rossmann
Key ref:
P.Zhang et al. (2008). Crystal structure of CD155 and electron microscopic studies of its complexes with polioviruses. Proc Natl Acad Sci U S A, 105, 18284-18289. PubMed id: 19011098 DOI: 10.1073/pnas.0807848105
Date:
29-Sep-08     Release date:   11-Nov-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P15151  (PVR_HUMAN) -  Poliovirus receptor
Seq:
Struc:
417 a.a.
213 a.a.*
Protein chain
Pfam   ArchSchema ?
P06210  (POLG_POL2L) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2207 a.a.
272 a.a.
Protein chain
Pfam   ArchSchema ?
P06210  (POLG_POL2L) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2207 a.a.
262 a.a.*
Protein chain
Pfam   ArchSchema ?
P06210  (POLG_POL2L) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2207 a.a.
68 a.a.
Protein chain
Pfam   ArchSchema ?
P06210  (POLG_POL2L) -  Genome polyprotein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2207 a.a.
235 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 2: Chains 1, 2, 4, 3: E.C.2.7.7.48  - RNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Nucleoside triphosphate
+ RNA(n)
= diphosphate
+ RNA(n+1)
   Enzyme class 3: Chains 1, 2, 4, 3: E.C.3.4.22.28  - Picornain 3C.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
   Enzyme class 4: Chains 1, 2, 4, 3: E.C.3.4.22.29  - Picornain 2A.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Selective cleavage of Tyr-|-Gly bond in the picornavirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
   Enzyme class 5: Chains 1, 2, 4, 3: E.C.3.6.1.15  - Nucleoside-triphosphate phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NTP + H2O = NDP + phosphate
NTP
+ H(2)O
= NDP
+ phosphate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     viral capsid   1 term 
  Biochemical function     structural molecule activity     1 term  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.0807848105 Proc Natl Acad Sci U S A 105:18284-18289 (2008)
PubMed id: 19011098  
 
 
Crystal structure of CD155 and electron microscopic studies of its complexes with polioviruses.
P.Zhang, S.Mueller, M.C.Morais, C.M.Bator, V.D.Bowman, S.Hafenstein, E.Wimmer, M.G.Rossmann.
 
  ABSTRACT  
 
When poliovirus (PV) recognizes its receptor, CD155, the virus changes from a 160S to a 135S particle before releasing its genome into the cytoplasm. CD155 is a transmembrane protein with 3 Ig-like extracellular domains, D1-D3, where D1 is recognized by the virus. The crystal structure of D1D2 has been determined to 3.5-A resolution and fitted into approximately 8.5-A resolution cryoelectron microscopy reconstructions of the virus-receptor complexes for the 3 PV serotypes. These structures show that, compared with human rhinoviruses, the virus-receptor interactions for PVs have a greater dependence on hydrophobic interactions, as might be required for a virus that can inhabit environments of different pH. The pocket factor was shown to remain in the virus during the first recognition stage. The present structures, when combined with earlier mutational investigations, show that in the subsequent entry stage the receptor moves further into the canyon when at a physiological temperature, thereby expelling the pocket factor and separating the viral subunits to form 135S particles. These results provide a detailed analysis of how a nonenveloped virus can enter its host cell.
 
  Selected figure(s)  
 
Figure 1.
Schematic presentation of human CD155α. The ectodomain is divided into the Ig-like D1, D2, and D3 domains (circles), followed by the transmembrane (TM) domain and the cytoplasmic domain (Cyt). The number of amino acids within each structural segment is indicated. The predicted N-glycosylation sites are depicted as open squares.
Figure 3.
Stereoviews showing the cryoEM reconstructions of PV1 complexed with deglycosylated CD155, viewed down an icosahedral 2-fold axis (Tables S1 and S2). The black triangle defines 1 icosahedral asymmetric unit on the viral surface.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22902367 O.J.Harrison, J.Vendome, J.Brasch, X.Jin, S.Hong, P.S.Katsamba, G.Ahlsen, R.B.Troyanovsky, S.M.Troyanovsky, B.Honig, and L.Shapiro (2012).
Nectin ectodomain structures reveal a canonical adhesive interface.
  Nat Struct Mol Biol, 19, 906-915.
PDB codes: 4fmf 4fmk 4fn0 4fom 4fqp 4frw 4fs0
22388738 X.Wang, W.Peng, J.Ren, Z.Hu, J.Xu, Z.Lou, X.Li, W.Yin, X.Shen, C.Porta, T.S.Walter, G.Evans, D.Axford, R.Owen, D.J.Rowlands, J.Wang, D.I.Stuart, E.E.Fry, and Z.Rao (2012).
A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71.
  Nat Struct Mol Biol, 19, 424-429.
PDB codes: 3vbf 3vbh 3vbo 3vbr 3vbs 3vbu
  21393840 H.Narita, A.Nakagawa, Y.Yamamoto, T.Sakisaka, Y.Takai, and M.Suzuki (2011).
Refolding, crystallization and preliminary X-ray crystallographic study of the whole extracellular regions of nectins.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 67, 344-348.  
20181687 H.C.Levy, M.Bostina, D.J.Filman, and J.M.Hogle (2010).
Catching a virus in the act of RNA release: a novel poliovirus uncoating intermediate characterized by cryo-electron microscopy.
  J Virol, 84, 4426-4441.
PDB codes: 3iyb 3iyc
19457456 C.J.Prust, P.C.Doerschuk, G.C.Lander, and J.E.Johnson (2009).
Ab initio maximum likelihood reconstruction from cryo electron microscopy images of an infectious virion of the tailed bacteriophage P22 and maximum likelihood versions of Fourier Shell Correlation appropriate for measuring resolution of spherical or cylindrical objects.
  J Struct Biol, 167, 185-199.  
19956667 T.S.Dermody, E.Kirchner, K.M.Guglielmi, and T.Stehle (2009).
Immunoglobulin superfamily virus receptors and the evolution of adaptive immunity.
  PLoS Pathog, 5, e1000481.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.