PDBsum entry 3kpe

Viral protein, fusion protein

PDB id: 3kpe

Contents

Protein chains

49 a.a. *

35 a.a. *

Ligands

TM3

PG4

Waters ×37

* Residue conservation analysis

PDB id:

3kpe

Name:

Viral protein, fusion protein

Title:

Solution structure of the respiratory syncytial virus (rsv)six-helix bundle complexed with tmc353121, a small-moleucule inhibitor of rsv

Structure:

Fusion glycoprotein f0. Chain: a. Fragment: proteinase k-resistant core of heptad repeat 1. Synonym: protein f, fusion glycoprotein f2, fusion glycoprotein f1. Fusion glycoprotein f0. Chain: b. Fragment: proteinase k-resistant core of heptad repeat 2. Synonym: protein f, fusion glycoprotein f2, fusion glycoprotein f1

Source:

Human respiratory syncytial virus. Organism_taxid: 11259. Strain: a2. Strain: a2

Resolution:

1.47Å R-factor: 0.165 R-free: 0.196

Authors:

D.Roymans,H.De Bondt,E.Arnoult,M.D.Cummings,H.Van Vlijmen,K.Andries

Key ref:

D.Roymans et al. (2010). Binding of a potent small-molecule inhibitor of six-helix bundle formation requires interactions with both heptad-repeats of the RSV fusion protein. Proc Natl Acad Sci U S A, 107, 308-313. PubMed id: 19966279 DOI: 10.1073/pnas.0910108106

Date:

16-Nov-09 Release date: 22-Dec-09

Protein chain

P03420  (FUS_HRSVA) -  Fusion glycoprotein F0 from Human respiratory syncytial virus A (strain A2)

Seq: 574 a.a.

Struc: 49 a.a.

Protein chain

P03420  (FUS_HRSVA) -  Fusion glycoprotein F0 from Human respiratory syncytial virus A (strain A2)

Seq: 574 a.a.

Struc: 35 a.a.

DOI no: 10.1073/pnas.0910108106

Proc Natl Acad Sci U S A 107:308-313 (2010)

PubMed id: 19966279

Binding of a potent small-molecule inhibitor of six-helix bundle formation requires interactions with both heptad-repeats of the RSV fusion protein.

D.Roymans, H.L.De Bondt, E.Arnoult, P.Geluykens, T.Gevers, M.Van Ginderen, N.Verheyen, H.Kim, R.Willebrords, J.F.Bonfanti, W.Bruinzeel, M.D.Cummings, H.van Vlijmen, K.Andries.

ABSTRACT

Six-helix bundle (6HB) formation is an essential step for many viruses that rely on a class I fusion protein to enter a target cell and initiate replication. Because the binding modes of small molecule inhibitors of 6HB formation are largely unknown, precisely how they disrupt 6HB formation remains unclear, and structure-based design of improved inhibitors is thus seriously hampered. Here we present the high resolution crystal structure of TMC353121, a potent inhibitor of respiratory syncytial virus (RSV), bound at a hydrophobic pocket of the 6HB formed by amino acid residues from both HR1 and HR2 heptad-repeats. Binding of TMC353121 stabilizes the interaction of HR1 and HR2 in an alternate conformation of the 6HB, in which direct binding interactions are formed between TMC353121 and both HR1 and HR2. Rather than completely preventing 6HB formation, our data indicate that TMC353121 inhibits fusion by causing a local disturbance of the natural 6HB conformation.

Selected figure(s)

Figure 4.
Binding mode and interaction map of TMC353121 and effect of the D486N mutation on the interactions. Binding mode of TMC353121 in the complete 6HB (A). The RSV 6HB is composed of three central HR1 helices (green surface) surrounded by three antiparallel HR2 helices (blue surface). The 6HB axis is tilted approximately 45 degrees from the plane of the page. Superimposition of the TMC353121 cocrystal structure with the 1G2C RSV 6HB crystal structure (B). The HR1 and HR2 helices of the cocrystal structure are dark green and blue, respectively, and the HR1 and HR2 helices from the 1G2C 6HB structure are shown in salmon and lilac, respectively. Displacement of sidechains by TMC353121 is indicated by orange arrows. Interaction map of TMC353121 with its 6HB target site (C). H-bonds are drawn as black dotted lines. Distances (Å) between interacting atoms are in black. TMC353121 makes a π–π stacking interaction with Y198. Residues from two neighboring HR1 or HR1’ and HR2 helices are indicated in green and blue, respectively. Effect of the HR2 resistance mutation D486N on electrostatic interactions in the TMC353121-bound 6HB complex (D). HR1 or HR1’ and HR2 residues are indicated in dark green and blue, respectively, and the calculated protein surface of HR1 and HR2 in transparent green and blue, respectively. HR2 residue 486 that causes resistance against TMC353121 upon mutation is shown in red. Orange arrows indicate hydrogen bonds. TMC353121 is colored by atom type (carbon = gray; oxygen = red; nitrogen = blue).

Figure 5.
Effect of TMC353121 on HR1/HR2-peptide interaction. Schematic representation of the different experimental conditions applied in the 6HB-ELISA (A). Influence of different concentrations of TMC353121 on the interaction between FITC-C39 with the HR1-CTC (B). The bars present tha data generated with three different experimental 6HB ELISA designs (orange = path 1; blue = path 2; green = path 3). Interaction between FITC-C39 and the HR1-CTC in the absence of TMC353121 was set at 100% (positive control), and the relative HR2 interaction with the HR1-CTC in the other conditions was normalized to this positive control condition. Values are from three independent experiments. P values and 95% confidence intervals are listed in Table S2.

Figures were selected by an automated process.