PDBsum entry 1qty

Hormone/growth factor receptor

PDB id: 1qty

Contents

Protein chains

95 a.a. *

94 a.a. *

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Solution structure of the vegf-Binding domain of flt-1: comparison of its free and bound states.

Authors

M.A.Starovasnik, H.W.Christinger, C.Wiesmann, M.A.Champe, A.M.De vos, N.J.Skelton.

Ref.

J Mol Biol, 1999, 293, 531-544. [DOI no: 10.1006/jmbi.1999.3134]

PubMed id

10543948

Abstract

The extracellular portion of the VEGF and PlGF receptor, Flt-1 (or VEGFR-1), consists of seven immunoglobulin-like domains. The second domain from the N terminus (Flt-1D2) is necessary and sufficient for high affinity VEGF binding. The 1.7 A resolution crystal structure of Flt-1D2 bound to VEGF revealed that this domain is a member of the I-set of the immunoglobulin superfamily, but has several unusual features including a region near the N terminus that bulges away from the domain rather than pairing with the neighboring beta-strand. Some of the residues in this region make contact with VEGF, raising the possibility that this bulge could be a consequence of VEGF binding and might not be present in the absence of ligand. Here we report the three-dimensional structure of Flt-1D2 in its uncomplexed form determined by NMR spectroscopy. A semi-automated method for NOE assignment that takes advantage of the previously solved crystal structure was used to facilitate rapid analysis of the 3D NOESY spectra. The solution structure is very similar to the previously reported VEGF-bound crystal structure; the N-terminal bulge is present, albeit in a different conformation. We also report the 2.7 A crystal structure of Flt-1D2 in complex with VEGF solved in a different crystal form that reveals yet another conformation for the N-terminal bulge region. (1)H-(15)N heteronuclear NOEs indicate this region is flexible in solution; the crystal structures show that this region is able to adopt more than one conformation even when bound to VEGF. Thus, VEGF-binding is not accompanied by significant structural change in Flt-1D2, and the unusual structural features of Flt-1D2 are an intrinsic property of this domain.

Figure 3.
Figure 3. Solution structure of Flt-1D2. The 20 final structures are shown superposed using backbone atoms of residues in the b-strands (colored red or blue). Strands are labeled as described (Wiesmann et al., 1997); the helical turn is colored green, and the disulfide bond buried in the core of the domain is colored yellow. This Figure and Figures 7-9 were generated using INSIGHT 97.0 (Molecular Simulations, Inc.).

Figure 6.
Figure 6. Ribbon diagram of the 2.7 Å resolution Flt-1D2/VEGF crystal structure. The two copies of Flt-1D2 are shown in blue; the two chains of the covalent VEGF dimer are shown in orange and yellow. (a) Side view, the membrane would be at the bottom in this orientation; (b) top view, 90 ° rotation from (a). This Figure was prepared using the program MOLSCRIPT (Kraulis, 1991).

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 293, 531-544) copyright 1999.

Secondary reference #1

Title

Crystal structure at 1.7 a resolution of vegf in complex with domain 2 of the flt-1 receptor.

Authors

C.Wiesmann, G.Fuh, H.W.Christinger, C.Eigenbrot, J.A.Wells, A.M.De vos.

Ref.

Cell, 1997, 91, 695-704. [DOI no: 10.1016/S0092-8674(00)80456-0]

PubMed id

9393862

Figure 2.
Figure 2. Ribbon Rendering of Flt-1[D2], in Two Views Related by a Rotation of Approximately 90° about the Vertical AxisThe termini and the secondary structure elements as defined by the program Procheck ([26]) are labeled; β strands are rendered as green arrows, the helical turn as a green ribbon, and the loop regions as gray tubes. The disulfide bond is shown in ball-and-stick rendering, with sulfur atoms colored yellow. The two potential N-linked glycosylation sites at Asn-164 and Asn-196 are colored blue. The VEGF binding site is located on the “bottom” end of the five-stranded sheet; residues in contact with VEGF in the complex are colored red. A segment near the N terminus, which forms strand βa in members of the I set of the immunoglobulin superfamily, bulges away from the core of the domain. This figure was created using the program MOLMOL ( [24]).

Figure 3.
Figure 3. Stereo Views in Ball-and-Stick Rendering of Structural DetailsHydrogen bonds are shown as dotted lines; oxygen atoms are colored red, nitrogens dark blue, and carbons gray. This figure was generated using the programs MOLSCRIPT ([25]) and RASTER3D ( [29]).(A) The environment of Phe-135 of Flt-1.(B) The region in Flt-1 corresponding to the “Y corner” found in most Greek key barrel proteins.(C) A region of the interface between VEGF (in dark gray) and Flt-1 (in light gray) around the interaction between Asp-63 and Arg-224, showing a chain of water molecules in the interface.

The above figures are reproduced from the cited reference with permission from Cell Press