Volume 9, Issue 3, Pages 255-266 (March 2001) The Structure of the Fusion Glycoprotein of Newcastle Disease Virus Suggests a Novel Paradigm for the Molecular Mechanism of Membrane Fusion  Lin Chen, Jeffrey J Gorman, Jenny McKimm-Breschkin, Lynne J Lawrence, Peter A Tulloch, Brian J Smith, Peter M Colman, Michael C Lawrence  Structure  Volume 9, Issue 3, Pages 255-266 (March 2001) DOI: 10.1016/S0969-2126(01)00581-0

Figure 1 Progressive Degradation of NDV-F, as Shown by 12% SDS-PAGE Analysis Lane 1: protein immediately after purification by gel filtration. Lane 2: protein immediately after purification by gel filtration + 5 mM dithiothreitol (DTT). Lane 3: protein stored at 4°C. Lane 4: protein stored at 4°C + 5 mM DTT. Lane 5: protein recovered from a single crystal dissolved after extensive washing. Lane 6: protein from same sample as Lane 5 + 5 mM DTT. The molecular weight of intact F0 is 60 kDa. Two lower molecular weight bands (at 50 kDa and 10 kDa) appear under reducing conditions; these species constitute ∼75% of the dissolved crystal material Structure 2001 9, 255-266DOI: (10.1016/S0969-2126(01)00581-0)

Figure 2 Overview of the X-Ray Structure of the NDV-F Trimer Left-hand panel: NDV-F viewed orthogonal to the three-fold molecular axis, with head uppermost. The dimensions of the three structural regions are indicated, as well as the location of the radial channel at the head-neck interface. Right-hand panel: NDV-F viewed down the three-fold axis, oriented with the head toward the viewer. The location of the axial channel is indicated. The three constituent monomers are colored red, mauve, and gold, respectively. The figure was generated using GRASP [48] Structure 2001 9, 255-266DOI: (10.1016/S0969-2126(01)00581-0)

Figure 3 Topology Diagram of the Head, Neck, and Stalk Regions of NDV-F, Including Schematic Representations of the Individual Domains within Each Monomer The β barrel domain I and the immunoglobulin-like domain II of the head are colored yellow and green, respectively. The central coiled-coil helix HR-A spans both the neck and stalk regions and is colored blue, as are β domain III and helix HR-C. Residues within domain III that originate from a neighboring monomer as well as the putative helix HR-B are colored light blue. The irregular four-helical bundle within the neck region is colored pink. Dashed lines and speckled regions indicate putative elements of the protein fold that are either not observed or interpretable in the electron density. The fusion peptide is shown as a zig-zag. The location of the native F2–F1 cleavage site (R116) and the site of proteolytic cleavage (S139) during sample preparation are indicated by a single and double scissors symbol, respectively. Individual domains are drawn in an arbitrary orientation for clarity, and their interconnection is indicated by placing a closed symbol at the C-terminal residue in one domain and the corresponding open symbol at the connecting N-terminal residue in the second domain (•→○, etc.). The figure was generated using MOLSCRIPT [49] and Raster3D [50] Structure 2001 9, 255-266DOI: (10.1016/S0969-2126(01)00581-0)

Figure 4 Stereo Backbone Trace of NDV-F as Observed in Our Structure (a) Monomer only, with every 20th residue and the observed termini labeled. The vertical lines indicate the three-fold axis, and the color scheme for individual domains corresponds to that of Figure 3. (b) Trimer, with individual monomers colored as in Figure 2. The figure was generated using MOLSCRIPT [49] Structure 2001 9, 255-266DOI: (10.1016/S0969-2126(01)00581-0)

Figure 5 Sequence Alignment of NDV-F with SV5-F Observed NDV-F secondary structural elements are included below the alignment in schematic form and are colored according to the scheme of Figure 3. Cysteine residues are highlighted in yellow. The locations of the observed N-linked glycosylation sites are indicated by tree symbols, and the locations of known escape mutations (see Table 1) are indicated by diamond symbols. The F2/F1 processing site is indicated by a single downward arrow, and the detected site of proteolytic degradation is indicated by a double downward arrow. The numbering above the sequences is that of NDV-F. The observed residues of the SV5-F-N1 and -C1 polypeptide segments [11] (122–184 and 440–477, respectively) are indicated by solid red lines. The figure was generated using ALSCRIPT [51] Structure 2001 9, 255-266DOI: (10.1016/S0969-2126(01)00581-0)

Figure 6 Schematic of the Superposition of the Structure of the SV5-F-N1/C1 Complex with the Stalk Region of NDV-F NDV-F elements are shown in transparent blue and light blue, following the color scheme of Figure 3; the SV5-F N1 HR-A segments are shown in red; and the SV5-F C1 HR-B segments are shown in orange. The superposition was obtained by minimizing the rmsd of the Cα coordinates of NDV-F HR-A residues G171–F190 with their corresponding counterparts in the SV5-F-N1/C1 complex (Figure 5). This alignment fits the N terminus of SV5-F HR-A into the opening of the central channel of the neighboring NDV-F trimer (shown in cutaway surface representation) located at (−1/2, 1/2, 0) within the crystal. The figure was produced using DINO [52] and Raster3D [50] Structure 2001 9, 255-266DOI: (10.1016/S0969-2126(01)00581-0)

Figure 7 Proposed Arrangement of the Fusion Peptide, HR-A, HR-B, and Transmembrane Anchor Elements of NDV-F in its Metastable Form and Stable Form (a) In the metastable (prefusion) form, the fusion peptide is proposed to be sequestered within the radial channels and linked to an N-terminally shortened HR-A via a predominantly extended polypeptide. The HR-B helices are likely unassociated. (b) In the stable (postfusion) form, the fusion peptide is located adjacent to the transmembrane anchor, and a full-length HR-A coiled coil is formed along the molecular axis with the HR-B helices packing antiparallel within its grooves. The pathway of transition between the two forms is unknown Structure 2001 9, 255-266DOI: (10.1016/S0969-2126(01)00581-0)

Figure 8 Stereo Diagram of a Portion of the Final Electron Density Map Obtained via Phase Extension to 3.5 Å Resolution Overlaid on the map are residues from the final model of NDV-F, including the C terminus of HR-A (residues 208–219 running bottom-to-top in the center of the diagram) as well as residues in the linker strand between domain II and the putative HR-B (residues 444–448 running top-to-bottom down the right-hand side of the diagram), with these latter residues being from a neighboring monomer. Overlaid on the (Fcalc,αcalc) map are residues from the side chains from adjacent HR-A segments that protrude into the map from the left. The figure was produced using MOLSCRIPT [49] Structure 2001 9, 255-266DOI: (10.1016/S0969-2126(01)00581-0)