PDBsum entry 1v9u

Virus/receptor

PDB id: 1v9u

Contents

Protein chains

269 a.a. *

250 a.a. *

237 a.a. *

25 a.a. *

39 a.a. *

Ligands

DAO

Metals

_CA

* Residue conservation analysis

PDB id:

1v9u

Name:

Virus/receptor

Title:

Human rhinovirus 2 bound to a fragment of its cellular receptor protein

Structure:

Coat protein vp1. Chain: 1. Synonym: p1d. Coat protein vp2. Chain: 2. Synonym: p1b. Coat protein vp3. Chain: 3. Synonym: p1c.

Source:

Human rhinovirus 2. Organism_taxid: 12130. Strain: serotype 2. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.60Å R-factor: 0.285 R-free: 0.295

Authors:

N.Verdaguer,I.Fita,M.Reithmayer,R.Moser,D.Blaas

Key ref:

N.Verdaguer et al. (2004). X-ray structure of a minor group human rhinovirus bound to a fragment of its cellular receptor protein. Nat Struct Mol Biol, 11, 429-434. PubMed id: 15064754 DOI: 10.1038/nsmb753

Date:

03-Feb-04 Release date: 04-May-04

Protein chain

P04936  (POLG_HRV2) -  Genome polyprotein from Human rhinovirus 2

Seq: 2150 a.a.

Struc: 269 a.a.

Protein chain

P04936  (POLG_HRV2) -  Genome polyprotein from Human rhinovirus 2

Seq: 2150 a.a.

Struc: 250 a.a.

Protein chain

P04936  (POLG_HRV2) -  Genome polyprotein from Human rhinovirus 2

Seq: 2150 a.a.

Struc: 237 a.a.

Protein chain

P04936  (POLG_HRV2) -  Genome polyprotein from Human rhinovirus 2

Seq: 2150 a.a.

Struc: 25 a.a.*

Protein chain

P98155  (VLDLR_HUMAN) -  Very low-density lipoprotein receptor from Homo sapiens

Seq: 873 a.a.

Struc: 39 a.a.

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: Chains 1, 2, 3, 4: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 2: Chains 1, 2, 3, 4: E.C.3.4.22.28 - picornain 3C.
• 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 3: Chains 1, 2, 3, 4: E.C.3.4.22.29 - picornain 2A.
• 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 4: Chains 1, 2, 3, 4: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺

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

reference

DOI no: 10.1038/nsmb753

Nat Struct Mol Biol 11:429-434 (2004)

PubMed id: 15064754

X-ray structure of a minor group human rhinovirus bound to a fragment of its cellular receptor protein.

N.Verdaguer, I.Fita, M.Reithmayer, R.Moser, D.Blaas.

ABSTRACT

Although many viral receptors have been identified, the ways in which they interact with their cognate viruses are not understood at the molecular level. We have determined the X-ray structure of a complex between calcium-containing modules of the very low-density lipoprotein receptor and the minor group human rhinovirus HRV2. The receptor binds close to the icosahedral five-fold vertex, with only one module per virus protomer. The binding face of this module is defined by acidic calcium-chelating residues and, in particular, by an exposed tryptophan that is highly conserved. The attachment site on the virus involves only residues from VP1, particularly a lysine strictly conserved in all minor group HRVs. The disposition of the attached ligand-binding repeats around the five-fold axis, together with the proximity of the N- and C-terminal ends of adjacent modules, suggests that more than one repeat in a single receptor molecule might attach simultaneously.

Selected figure(s)

Figure 1.
Figure 1. Scheme of the modular organization of members of the LDLR family. LDLR and VLDLR have seven and eight N-terminal ligand binding repeats, L1 -L7 and V1 -V8, respectively. Three epidermal growth factor precursor-like regions (A -C) flank a six-bladed -propeller ( ) with YWTD motifs. The adjacent domain (GLYCO) carries O-linked oligosaccharides. The receptors are anchored in the membrane via a single transmembrane domain (TM). The intracellular C termini carry NPXY clathrin-localization signals.

Figure 2.
Figure 2. Three-dimensional structure of the V23 -HRV2 complex. (a) Stereo view of the 3.5 Å -averaged electron density of V3 bound to HRV2. The region corresponds to residues from His13 to Glu36 of the V3 receptor. The V3 model is also shown in ball-and-stick representation. The Ca^2+ ion in the center of the acidic cluster is green. Residues involved directly in interactions with HRV2 are labeled. (b) Orthogonal views of an HRV2-V3 pentamer subunit. HRV2 proteins are shown as space-filling model colored in the standard viral protein color code (VP1, blue, VP2, green and VP3, red) in the reference protomer and light blue in the others. The five V3 receptors are shown as worms in yellow.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2004, 11, 429-434) copyright 2004.

Figures were selected by an automated process.