PDBsum entry 2cme

Hypothetical protein

PDB id: 2cme

Contents

Protein chains

78 a.a.

(+ 1 more) 79 a.a.

Ligands

D10 ×4

Waters ×7

References listed in PDB file

Key reference

Title

The crystal structure of orf-9b, A lipid binding protein from the sars coronavirus.

Authors

C.Meier, A.R.Aricescu, R.Assenberg, R.T.Aplin, R.J.Gilbert, J.M.Grimes, D.I.Stuart.

Ref.

Structure, 2006, 14, 1157-1165. [DOI no: 10.1016/j.str.2006.05.012]

PubMed id

16843897

Abstract

To achieve the greatest output from their limited genomes, viruses frequently make use of alternative open reading frames, in which translation is initiated from a start codon within an existing gene and, being out of frame, gives rise to a distinct protein product. These alternative protein products are, as yet, poorly characterized structurally. Here we report the crystal structure of ORF-9b, an alternative open reading frame within the nucleocapsid (N) gene from the SARS coronavirus. The protein has a novel fold, a dimeric tent-like beta structure with an amphipathic surface, and a central hydrophobic cavity that binds lipid molecules. This cavity is likely to be involved in membrane attachment and, in mammalian cells, ORF-9b associates with intracellular vesicles, consistent with a role in the assembly of the virion. Analysis of ORF-9b and other overlapping genes suggests that they provide snapshots of the early evolution of novel protein folds.

Figure 1.
Figure 1. The Structure of the SARS-CoV Genome
Alternative open reading frames (ORF-3b, -7b, -8b, and -9b) are highlighted in gray. The nucleocapsid (N) gene including its internal alternative open reading frame, ORF-9b, is shown in an enlarged representation. S, spike protein; 3, ORF-3; E, envelope protein; M, membrane protein; 6, ORF-6; 7, ORF-7; 8, ORF-8; N, nucleocapsid protein (adapted from Snijder et al., 2003; genome representation is not to scale).

Figure 5.
Figure 5. The Structural Evolution of Alternative Open Reading Frames in Viruses
(A) The evolution of coronaviruses (adapted from Snijder et al., 2003). Based on their genome sequence, coronaviruses fall into three main groups. SARS-CoV is thought to be an early split-off from the group 2 lineage (indicated by a dashed circle). Alternative open reading frames of the nucleocapsid gene are found only in group 2 viruses, such as MHV and BCV (Senanayake and Brian, 1997), as well as group 2-related viruses, including SARS-CoV. BCV, bovine coronavirus; HCoV-229E, human coronavirus 229E; IBV, infectious bronchitis virus; MHV, murine hepatitis virus; PDEV, porcine epidemic diarrhea virus; SARS-CoV, severe acute respiratory syndrome coronavirus; TGEV, transmissible gastroenteritis virus.
(B) A model for the structural evolution of ORF-9b within the SARS-CoV N-gene. Starting from an N-gene without an alternative ORF, the protein first arises as an “accidental” translation product, which is mostly unstructured. By gradual constrained evolution, it becomes increasingly structured, eventually attaining its present fold. In this scheme, disordered regions (colored in red) are a relict of the evolutionary trajectory of the protein. The N-protein is represented as a composite of two NMR structures of its well-conserved N- and C-terminal domains ([Chang et al., 2005a] and [Huang et al., 2004]), which are thought to be surrounded by flexible linkers (Chang et al., 2005b) (colored in red). The region of the N-terminal domain which overlaps with ORF-9b is shown in green.
(C) For comparison, an illustration of the HIV1 vpu and env genes, which partially overlap. The NMR structure of the overlapping portion of VPU (Willbold et al., 1997) (PDB code: 1VPU) is shown. This protein is relatively poorly ordered (rmsd = 1.6 Å between multiple determinations of the fold, for all Cα atoms). The least ordered regions (rmsd > 2 Å) are highlighted in red.

The above figures are reprinted by permission from Cell Press: Structure (2006, 14, 1157-1165) copyright 2006.