PDBsum entry: 1aj7

Immunoglobulin

PDB-id: 1aj7

Biological unit* = asymmetric unit, as shown
(*as deduced by PQS)

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Description

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References

PROCHECK

Protein chains

214 a.a. *

217 a.a. *

Ligands

NPE

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

1aj7

Name:

Immunoglobulin

Title:

Immunoglobulin 48g7 germline fab antibody complexed with hapten 5-(para-nitrophenyl phosphonate)-pentanoic acid. Affinity maturation of an esterolytic antibody

Structure:

Immunoglobulin 48g7 fab (light chain). Chain: l. Fragment: variable domains of light and heavy chains and constant domains of light and heavy chains. Engineered: yes. Immunoglobulin 48g7 fab (heavy chain). Chain: h. Fragment: variable domains of light and heavy chains and constant domains of light and heavy chains.

Source:

Fragment: constant domains of light and heavy chains. Mus musculus. House mouse. Organism_taxid: 10090. Cell_line: 48g7. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Other_details: each chain is a fusion polypeptide which is part human and part mouse.

Biological unit:

Dimer (from PQS)

UniProt:

Chain H: P01857 (IGHG1_HUMAN)

Seq:

Struc:

Seq:

330 a.a.

Struc:

217 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Resolution:

2.10Å

R-factor:

0.217

R-free:

0.258

Authors:

G.J.Wedemayer,L.H.Wang,P.A.Patten,P.G.Schultz,R.C.Stevens

Key ref:

G.J.Wedemayer et al. (1997). Structural insights into the evolution of an antibody combining site.. Science, 276, 1665-1669. [PubMed id: 9180069] [DOI: 10.1126/science.276.5319.1665]

Date:

15-May-97

Release date:

12-Nov-97

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Clefts

Surface

Key reference

DOI no: 10.1126/science.276.5319.1665

Science 276:1665-1669 (1997)

PubMed id: 9180069

Structural insights into the evolution of an antibody combining site.

G.J.Wedemayer, P.A.Patten, L.H.Wang, P.G.Schultz, R.C.Stevens.

ABSTRACT

The crystal structures of a germline antibody Fab fragment and its complex with hapten have been solved at 2.1 A resolution. These structures are compared with the corresponding crystal structures of the affinity-matured antibody, 48G7, which has a 30,000 times higher affinity for hapten as a result of nine replacement somatic mutations. Significant changes in the configuration of the combining site occur upon binding of hapten to the germline antibody, whereas hapten binds to the mature antibody by a lock-and-key fit mechanism. The reorganization of the combining site that was nucleated by hapten binding is further optimized by somatic mutations that occur up to 15 from bound hapten. These results suggest that the binding potential of the primary antibody repertoire may be significantly expanded by the ability of germline antibodies to adopt more than one combining-site configuration, with both antigen binding and somatic mutation stabilizing the configuration with optimal hapten complementarity.

Selected figure(s)

Figure 1.
Fig. 1. Ribbon superpositions of the variable regions of the germline Fab-hapten complex (light purple) and mature Fab-hapten complex (dark red). The aliphatic linker used to conjugate the hapten to the carrier protein can be seen extending toward the top of^ the figure. The side chains of the somatic mutation sites are^ indicated in light green (germ line) and dark green (mature) (SerL30 Asn, SerL34 Gly, AspL55 His, GluH42 Lys, GlyH55 Val, AsnH56 Asp, GlyH65 Asp, AsnH76 Lys, Ala^H78 Thr).

Figure 2.
Fig. 2. Superposition of the structures of the germline Fab without hapten (light blue) and the germline Fab-hapten complex (light purple), illustrating the structural changes that occur on hapten binding to the germline Fab. In all figures, the aliphatic linker of the hapten has been omitted for clarity. Gray dotted lines denote hydrogen bonds in the structure of the germline Fab without hapten, while black dotted lines denote hydrogen bonds in the^ germline Fab-hapten complex. (A) CDR3 of the heavy chain is reorganized on hapten binding. To make room for the hapten, the side chain of TyrH99 moves 6 Å away from the hapten. The side chain of TyrH98 moves 8.3 Å and inserts between TyrH99 and TyrH33, and TyrH33 moves toward the phosphonate group. These movements establish a -cation interaction between the side chains of ArgL46 and TyrH99, a - interaction between the aryl groups of TyrH99 and TyrH98, and a T-stack interaction between the aryl rings of TyrH98 and TyrH33 (yellow dotted lines). In addition, the ArgL46 side chain is stabilized by salt bridges to the AspL55 carboxylate group and to the TyrH99 main chain carbonyl group. (B) The interactions between residues in CDR1, CDR2, and CDR3 of the heavy chain in the germline^ Fab structures. The side chain of ArgH50 forms hydrogen bonds to the hydroxyl groups of TyrH33 and TyrL94 upon hapten binding. The guanidinium group of ArgH50 is positioned by a hydrogen bond with AsnH56. Although TyrH33 forms one hydrogen bond to ArgH50, it does not interact directly with either TyrL94 or the bound hapten, nor does LysH58 interact with residue H56 (cf. Fig. 3B). (C) Closeup of^ the combining site showing the orientations of the residues directly involved in hapten binding in the germline-hapten complex HisH35, TyrH33, and ArgL96. All four hydrogen bonds are directed to the oxygens (red) of^ the phosphonate group (phosphorus-yellow). TyrH33 moves 2.2 Å toward the phosphonate group, which is a key binding determinant in the hapten and is located in approximately the^ same position in the combining sites of the germline and affinity-matured^ Fab-hapten complexes.

The above figures are reprinted by permission from the AAAs: Science (1997, 276, 1665-1669) copyright 1997.

Figures were selected by the author.