PDBsum entry 1aym

Virus

PDB id: 1aym

Contents

Protein chains

285 a.a. *

252 a.a. *

238 a.a. *

29 a.a. *

Ligands

DAO

MYR

Metals

_ZN

Waters ×533

* Residue conservation analysis

PDB id:

1aym

Name:

Virus

Title:

Human rhinovirus 16 coat protein at high resolution

Structure:

Human rhinovirus 16 coat protein. Chain: 1. Synonym: hrv16. Engineered: yes. Mutation: yes. Human rhinovirus 16 coat protein. Chain: 2. Synonym: hrv16. Engineered: yes.

Source:

Human rhinovirus sp.. Organism_taxid: 169066. Strain: serotype 16. Cell_line: hela. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_taxid: 9606

Resolution:

2.15Å R-factor: 0.230 R-free: 0.233

Authors:

A.T.Hadfield,M.G.Rossmann

Key ref:

A.T.Hadfield et al. (1997). The refined structure of human rhinovirus 16 at 2.15 A resolution: implications for the viral life cycle. Structure, 5, 427-441. PubMed id: 9083115 DOI: 10.1016/S0969-2126(97)00199-8

Date:

06-Nov-97 Release date: 21-Jan-98

Protein chain

Q82122  (POLG_HRV16) -  Genome polyprotein from Human rhinovirus 16

Seq: 2153 a.a.

Struc: 285 a.a.

Protein chain

Q82122  (POLG_HRV16) -  Genome polyprotein from Human rhinovirus 16

Seq: 2153 a.a.

Struc: 252 a.a.

Protein chain

Q82122  (POLG_HRV16) -  Genome polyprotein from Human rhinovirus 16

Seq: 2153 a.a.

Struc: 238 a.a.

Protein chain

P23008  (POLG_HRV1A) -  Genome polyprotein from Human rhinovirus 1A

Seq: 2157 a.a.

Struc: 29 a.a.

Enzyme reactions

• Enzyme class 2: 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 3: 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 4: 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 5: 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: 10.1016/S0969-2126(97)00199-8

Structure 5:427-441 (1997)

PubMed id: 9083115

The refined structure of human rhinovirus 16 at 2.15 A resolution: implications for the viral life cycle.

A.T.Hadfield, W.Lee, R.Zhao, M.A.Oliveira, I.Minor, R.R.Rueckert, M.G.Rossmann.

ABSTRACT

BACKGROUND: Rhinoviruses belong to the picornavirus family and are small, icosahedral, non-enveloped viruses containing one positive RNA strand. Human rhinovirus 16 (HRV16) belongs to the major receptor group of rhinoviruses, for which the cellular receptor is intercellular adhesion molecule-1 (ICAM-1). In many rhinoviruses, one of the viral coat proteins (VP1) contains a hydrophobic pocket which is occupied by a fatty acid-like molecule, or so-called 'pocket factor'. Antiviral agents have been shown to bind to the hydrophobic pocket in VP1, replacing the pocket factor. The presence of the antiviral compound blocks uncoating of the virus and in some cases inhibits receptor attachment. A refined, high-resolution structure would be expected to provide further information on the nature of the pocket factor and other features previously not clearly identified. RESULTS: The structure of native HRV16 has been refined to a resolution of 2.15 A. The hydrophobic pocket in VP1 is observed in two alternative conformations. In one of these, the pocket is filled by a pocket factor and the protein structure is similar to virus-antiviral compound complexes. In the other conformation, the hydrophobic pocket is collapsed and empty. RNA bases stack against both a tryptophan and a phenylalanine residue on the internal surface of the viral capsid. Site-directed mutagenesis of the tryptophan, which is conserved across the picornaviruses, to nonconservative residues results in non-viable virus. Five symmetry-related N termini of coat protein VP4 form a ten-stranded, antiparallel beta barrel around the base of the icosahedral fivefold axis. The N termini of VP1 are amphipathic alpha helices, which stack on the outside of this beta barrel. The N termini of VP1 and VP4 have not been observed previously in rhinovirus structures. CONCLUSIONS: The observation of a partially occupied hydrophobic pocket in HRV16 forms a missing link between HRV14, which is always observed with no pocket factor in the native form, and rhinovirus 1A and other picornaviruses (e.g. poliovirus, coxsackievirus) which contain pocket factors. The pocket factor molecules probably regulate viral entry, uncoating and assembly. Picornavirus assembly is known to proceed via pentamers, therefore, the interaction of RNA with the conserved tryptophan residues across twofold axes between pentamers may play a role in picornavirus assembly. The positioning of a cation on the icosahedral fivefold axes and the structure of the N termini of VP4 and VP1 around these axes suggest a mechanism for the uncoating of rhinoviruses.

Selected figure(s)

Figure 6.
Figure 6. A schematic diagram representing VP1 of HRV16, showing the binding site of the pocket factor (shown in ball-and-stick representation) and the WIN antiviral compounds (shown in pale blue). A cation on the fivefold axis is shown in yellow. The N termini of VP1, VP3 and VP4 also interact around the fivefold axis. One copy of each of VP1 and the N termini of VP3 and VP4 are shown as blue, red and green ribbon diagrams, respectively. The myristylated N terminus of VP4 is labelled (MYR). (The diagram was created using MOLSCRIPT [64].)

The above figure is reprinted by permission from Cell Press: Structure (1997, 5, 427-441) copyright 1997.

Figure was selected by an automated process.