PDBsum entry 1k5m

Virus

PDB id: 1k5m

Contents

Protein chains

283 a.a. *

270 a.a. *

236 a.a. *

40 a.a. *

Ligands

SPH

Waters ×637

* Residue conservation analysis

PDB id:

1k5m

Name:

Virus

Title:

Crystal structure of a human rhinovirus type 14:human immunodeficiency virus type 1 v3 loop chimeric virus mn-iii-2

Structure:

Coat protein vp1 (p1d). Chain: a. Engineered: yes. Chimera of hrv14 coat protein vp2 (p1b) and the v3 loop of HIV-1 gp120. Chain: b. Engineered: yes. Other_details: the chimera consists of the hrv14 coat protein vp2 (p1b) and residues 314-325 of HIV-1 gp120..

Source:

Human rhinovirus 14. Organism_taxid: 12131. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: h1-hela cells. Human rhinovirus 14, human immunodeficiency virus type 1 group m subtype b (isolate mn). HIV-1. Organism_taxid: 12131, 11696.

Resolution:

2.70Å R-factor: 0.216

Authors:

J.Ding,A.D.Smith,S.C.Geisler,X.Ma,G.F.Arnold,E.Arnold

Key ref:

J.Ding et al. (2002). Crystal structure of a human rhinovirus that displays part of the HIV-1 V3 loop and induces neutralizing antibodies against HIV-1. Structure, 10, 999. PubMed id: 12121655 DOI: 10.1016/S0969-2126(02)00793-1

Date:

11-Oct-01 Release date: 17-Jul-02

Protein chain

P03303  (POLG_HRV14) -  Genome polyprotein from Human rhinovirus 14

Seq: 2179 a.a.

Struc: 283 a.a.

Protein chain

P03303  (POLG_HRV14) -  Genome polyprotein from Human rhinovirus 14

Seq: 2179 a.a.

Struc: 270 a.a.*

Protein chain

P05877  (ENV_HV1MN) -  Envelope glycoprotein gp160 from Human immunodeficiency virus type 1 group M subtype B (isolate MN)

Seq: 856 a.a.

Struc: 270 a.a.*

Protein chain

P03303  (POLG_HRV14) -  Genome polyprotein from Human rhinovirus 14

Seq: 2179 a.a.

Struc: 236 a.a.

Protein chain

P03303  (POLG_HRV14) -  Genome polyprotein from Human rhinovirus 14

Seq: 2179 a.a.

Struc: 40 a.a.

* PDB and UniProt seqs differ at 252 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, B, C, D: 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 A, B, C, D: 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 A, B, C, D: 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 A, B, C, D: 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(02)00793-1

Structure 10:999 (2002)

PubMed id: 12121655

Crystal structure of a human rhinovirus that displays part of the HIV-1 V3 loop and induces neutralizing antibodies against HIV-1.

J.Ding, A.D.Smith, S.C.Geisler, X.Ma, G.F.Arnold, E.Arnold.

ABSTRACT

We report the 2.7 A resolution structure of a chimeric rhinovirus, MN-III-2, that displays part of the HIV-1 gp120 V3 loop and elicits HIV-neutralizing antibodies. The V3 loop insert is dominated by two type I beta turns. The structures of two adjacent tripeptides resemble those of analogous segments in three Fab/V3 loop peptide complexes. Although two of the three corresponding antibodies bind and neutralize MN-III-2 well, only one of the three can bind without significant rearrangement. These results suggest that the V3 loop insert: (1) can share some local conformational similarity to V3 loop sequences presented on different structural frameworks; (2) must be able to adopt multiple conformations, even in a relatively constrained environment; and (3) may mimic the conformational variability of the epitope on HIV-1, increasing the likelihood of eliciting appropriate neutralizing immune responses.

Selected figure(s)

Figure 5.
Figure 5. The Pocket Factor, Sphingosine (Shown as a Green Ball-and-Stick Model), in the Binding Pocket of VP1 Located below the External Canyon Region where Host Cell Receptor Binding OccursVP1 and VP3 are shown in blue and red ribbons, respectively. The side chains of the surrounding amino acid residues that have close contacts with sphingosine are shown. The interactions between sphingosine and the amino acid residues are primarily hydrophobic in nature (=<3.6 Å, indicated with dashed lines). Hydrogen bonds are indicated with solid lines.

The above figure is reprinted by permission from Cell Press: Structure (2002, 10, 999-0) copyright 2002.

Figure was selected by an automated process.