PDBsum entry 1tzh

Immune system

PDB id: 1tzh

Contents

Protein chains

94 a.a. *

210 a.a. *

222 a.a. *

Waters ×110

* Residue conservation analysis

PDB id:

1tzh

Name:

Immune system

Title:

Crystal structure of the fab yads1 complexed with h-vegf

Structure:

Vascular endothelial growth factor a. Chain: v, w. Synonym: vegf-a, vascular permeability factor, vpf, h-vegf. Engineered: yes. Fab yads1 light chain. Chain: a, l. Engineered: yes. Fab yads1 heavy chain. Chain: b, h.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: vegf, vegfa. Expressed in: escherichia coli. Expression_system_taxid: 562. Mus musculus. House mouse. Organism_taxid: 10090.

Biol. unit:

Hexamer (from PQS)

Resolution:

2.60Å R-factor: 0.215 R-free: 0.271

Authors:

F.A.Fellouse,C.Wiesmann,S.S.Sidhu

Key ref:

F.A.Fellouse et al. (2004). Synthetic antibodies from a four-amino-acid code: a dominant role for tyrosine in antigen recognition. Proc Natl Acad Sci U S A, 101, 12467-12472. PubMed id: 15306681 DOI: 10.1073/pnas.0401786101

Date:

09-Jul-04 Release date: 31-Aug-04

Protein chains

P15692  (VEGFA_HUMAN) -  Vascular endothelial growth factor A, long form from Homo sapiens

Seq: 395 a.a.

Struc: 94 a.a.

Protein chains

No UniProt id for this chain

Struc: 210 a.a.

Protein chains

No UniProt id for this chain

Struc: 222 a.a.

DOI no: 10.1073/pnas.0401786101

Proc Natl Acad Sci U S A 101:12467-12472 (2004)

PubMed id: 15306681

Synthetic antibodies from a four-amino-acid code: a dominant role for tyrosine in antigen recognition.

F.A.Fellouse, C.Wiesmann, S.S.Sidhu.

ABSTRACT

Antigen-binding fragments (Fabs) with synthetic antigen-binding sites were isolated from phage-displayed libraries with restricted complementarity-determining region (CDR) diversity. Libraries were constructed such that solvent-accessible CDR positions were randomized with a degenerate codon that encoded for only four amino acids (tyrosine, alanine, aspartate, and serine). Nonetheless, high-affinity Fabs (K(d) = 2-10 nM) were isolated against human vascular endothelial growth factor (hVEGF), and the crystal structures were determined for two distinct Fab-hVEGF complexes. The structures revealed that antigen recognition was mediated primarily by tyrosine side chains, which accounted for 71% of the Fab surface area that became buried upon binding to hVEGF. In contrast, aspartate residues within the CDRs were almost entirely excluded from the binding interface. Alanine and serine residues did not make many direct contacts with antigen, but they allowed for space and conformational flexibility and thus played an auxiliary role in facilitating productive contacts between tyrosine and antigen. Tyrosine side chains were capable of mediating most of the contacts necessary for high-affinity antigen recognition, and, thus, it seems likely that the overabundance of tyrosine in natural antigen-binding sites is a consequence of the side chain being particularly well suited for making productive contacts with antigen. The findings shed light on the basic principles governing the evolution of natural immune repertoires and should also aid the development of improved synthetic antibody libraries.

Selected figure(s)

Figure 3.
Fig. 3. The structural epitope for binding to YADS1 (A) or YADS2 (B) mapped on the molecular surface of hVEGF. The structural epitope consists of hVEGF residues that make contact with one or more residues of the Fab, with "contact" defined as a distance <4.1 Å. Residues that contact the heavy or light chain are colored green or yellow, respectively. The dashed line outlines the structural epitope for binding to Flt-1[D2], as determined from a previously described x-ray structure (PDB code 1FLT [PDB] ) (34).

Figure 5.
Fig. 5. The CDR side chains of YADS1 (A) and YADS2 (B) that contact hVEGF. The structural epitope for binding to the Fab (see Fig. 3) was mapped onto the molecular surface of hVEGF, and residues that made contacts with tyrosines or other residue types are colored orange or blue, respectively. The side chains at CDR positions that were randomized in the libraries are shown. Side chains that do not make contact with hVEGF are colored white. Tyrosine side chains that make contacts with hVEGF are colored red, whereas all other contacting side chains are colored blue. The hVEGF molecules are shown in the same orientation in both panels.

Figures were selected by an automated process.