PDBsum entry 1zv8

Viral protein

PDB id: 1zv8

Contents

Protein chains

49 a.a. *

27 a.a. *

46 a.a. *

29 a.a. *

30 a.a. *

50 a.a. *

34 a.a. *

34 a.a. *

Ligands

CAC

ACT

Metals

_NA ×6

_ZN ×2

Waters ×176

* Residue conservation analysis

PDB id:

1zv8

Name:

Viral protein

Title:

A structure-based mechanism of sars virus membrane fusion

Structure:

E2 glycoprotein. Chain: a, c, e, g, i, k. Fragment: residues 901-950. Synonym: spike glycoprotein, peplomer protein. Engineered: yes. E2 glycoprotein. Chain: b, d, f, h, j, l. Fragment: residues 1150-1185. Synonym: spike glycoprotein, peplomer protein.

Source:

Sars coronavirus. Organism_taxid: 227859. Strain: sars. Gene: s. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Hexamer (from PQS)

Resolution:

1.94Å R-factor: 0.207 R-free: 0.274

Authors:

Y.Deng,J.Liu,Q.Zheng,W.Yong,J.Dai,M.Lu

Key ref:

Y.Deng et al. (2006). Structures and polymorphic interactions of two heptad-repeat regions of the SARS virus S2 protein. Structure, 14, 889-899. PubMed id: 16698550 DOI: 10.1016/j.str.2006.03.007

Date:

01-Jun-05 Release date: 16-May-06

Protein chains

P59594  (SPIKE_CVHSA) -  Spike glycoprotein from Severe acute respiratory syndrome coronavirus

Seq: 1255 a.a.

Struc: 49 a.a.

Protein chain

P59594  (SPIKE_CVHSA) -  Spike glycoprotein from Severe acute respiratory syndrome coronavirus

Seq: 1255 a.a.

Struc: 27 a.a.

Protein chain

P59594  (SPIKE_CVHSA) -  Spike glycoprotein from Severe acute respiratory syndrome coronavirus

Seq: 1255 a.a.

Struc: 46 a.a.

Protein chain

P59594  (SPIKE_CVHSA) -  Spike glycoprotein from Severe acute respiratory syndrome coronavirus

Seq: 1255 a.a.

Struc: 29 a.a.

Protein chains

P59594  (SPIKE_CVHSA) -  Spike glycoprotein from Severe acute respiratory syndrome coronavirus

Seq: 1255 a.a.

Struc: 30 a.a.

Protein chains

P59594  (SPIKE_CVHSA) -  Spike glycoprotein from Severe acute respiratory syndrome coronavirus

Seq: 1255 a.a.

Struc: 50 a.a.

Protein chain

P59594  (SPIKE_CVHSA) -  Spike glycoprotein from Severe acute respiratory syndrome coronavirus

Seq: 1255 a.a.

Struc: 34 a.a.

Protein chain

P59594  (SPIKE_CVHSA) -  Spike glycoprotein from Severe acute respiratory syndrome coronavirus

Seq: 1255 a.a.

Struc: 34 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L: E.C.?

DOI no: 10.1016/j.str.2006.03.007

Structure 14:889-899 (2006)

PubMed id: 16698550

Structures and polymorphic interactions of two heptad-repeat regions of the SARS virus S2 protein.

Y.Deng, J.Liu, Q.Zheng, W.Yong, M.Lu.

ABSTRACT

Entry of SARS coronavirus into its target cell requires large-scale structural transitions in the viral spike (S) glycoprotein in order to induce fusion of the virus and cell membranes. Here we describe the identification and crystal structures of four distinct alpha-helical domains derived from the highly conserved heptad-repeat (HR) regions of the S2 fusion subunit. The four domains are an antiparallel four-stranded coiled coil, a parallel trimeric coiled coil, a four-helix bundle, and a six-helix bundle that is likely the final fusogenic form of the protein. When considered together, the structural and thermodynamic features of the four domains suggest a possible mechanism whereby the HR regions, initially sequestered in the native S glycoprotein spike, are released and refold sequentially to promote membrane fusion. Our results provide a structural framework for understanding the control of membrane fusion and should guide efforts to intervene in the SARS coronavirus entry process.

Selected figure(s)

Figure 3.
Figure 3. Crystal Structure of the C44 Tetramer
(A) Lateral view of the C44 tetramer. Yellow van der Waals surfaces identify residues at the a positions, red surfaces identify residues at the d positions, and light-blue surfaces identify residues at the g positions. The N termini of helices A and B are indicated.
(B) Axial view of the C44 tetramer. The red van der Waals surfaces of the Ile1154(d) and Leu1182(d) side chains are depicted.
(C) Cross-section of the tetramer in the Ile1161(d) layer. The 1.70 Å 2F[o] − F[c] electron density map (contoured at 1.2σ) is shown with the refined molecular model.
(D) Helical wheel representation of residues 1153–1185 of the C44 tetramer. Heptad-repeat positions are labeled a–g. The C44 helices interact through a previously uncharacterized type of packing interaction between the a, d, and g side chains (colored green). Figure 3. Crystal Structure of the C44 Tetramer(A) Lateral view of the C44 tetramer. Yellow van der Waals surfaces identify residues at the a positions, red surfaces identify residues at the d positions, and light-blue surfaces identify residues at the g positions. The N termini of helices A and B are indicated.(B) Axial view of the C44 tetramer. The red van der Waals surfaces of the Ile1154(d) and Leu1182(d) side chains are depicted.(C) Cross-section of the tetramer in the Ile1161(d) layer. The 1.70 Å 2F[o] − F[c] electron density map (contoured at 1.2σ) is shown with the refined molecular model.(D) Helical wheel representation of residues 1153–1185 of the C44 tetramer. Heptad-repeat positions are labeled a–g. The C44 helices interact through a previously uncharacterized type of packing interaction between the a, d, and g side chains (colored green).

Figure 5.
Figure 5. Crystal Structure of the N50/C36 Complex
(A) Ribbon diagram of the N50/C36 complex. The N termini of the N50 (red) and C36 (green) chains are indicated.
(B) Conserved grooves on the surface of the N50 coiled-coil trimer. The C36 peptides drawn as an atomic model are shown against a surface representation of the N50 trimer. The view is in approximately the same orientation as in (A). The solvent-accessible surface is colored according to the local electrostatic potential; colors range from dark blue, representing the most positive area, to deep red, representing the most negative area.
(C) Cross-section of the N50/C36 complex in the Thr923 layer showing “x-like” packing of side chains that project simultaneously toward the 3-fold axis. The 2F[o] − F[c] electron density map contoured at 1.5σ is shown with the refined molecular model.
(D) Cross-section of the N50/C36 complex in the Ser919–Leu920 layer showing “y-like” packing of alternating small and large side chains in a hexagonal arrangement. Figure 5. Crystal Structure of the N50/C36 Complex(A) Ribbon diagram of the N50/C36 complex. The N termini of the N50 (red) and C36 (green) chains are indicated.(B) Conserved grooves on the surface of the N50 coiled-coil trimer. The C36 peptides drawn as an atomic model are shown against a surface representation of the N50 trimer. The view is in approximately the same orientation as in (A). The solvent-accessible surface is colored according to the local electrostatic potential; colors range from dark blue, representing the most positive area, to deep red, representing the most negative area.(C) Cross-section of the N50/C36 complex in the Thr923 layer showing “x-like” packing of side chains that project simultaneously toward the 3-fold axis. The 2F[o] − F[c] electron density map contoured at 1.5σ is shown with the refined molecular model.(D) Cross-section of the N50/C36 complex in the Ser919–Leu920 layer showing “y-like” packing of alternating small and large side chains in a hexagonal arrangement.

The above figures are reprinted by permission from Cell Press: Structure (2006, 14, 889-899) copyright 2006.

Figures were selected by an automated process.