PDBsum entry 12e8

Immunoglobulin

PDB id: 12e8

Contents

Protein chains

214 a.a. *

221 a.a. *

Waters ×767

* Residue conservation analysis

PDB id:

12e8

Name:

Immunoglobulin

Title:

2e8 fab fragment

Structure:

Igg1-kappa 2e8 fab (light chain). Chain: l, m. Fragment: fab fragment. Igg1-kappa 2e8 fab (heavy chain). Chain: h, p. Fragment: fab fragment

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Strain: balb/c. Cell_line: 2e8 hybridoma. Organ: spleen. Cell: lymphocyte-plasma cell. Cell: lymphocyte-plasma cell

Biol. unit:

Dimer (from PQS)

Resolution:

1.90Å R-factor: 0.221 R-free: 0.271

Authors:

B.Rupp,S.Trakhanov

Key ref:

S.Trakhanov et al. (1999). Structure of a monoclonal 2E8 Fab antibody fragment specific for the low-density lipoprotein-receptor binding region of apolipoprotein E refined at 1.9 A. Acta Crystallogr D Biol Crystallogr, 55, 122-128. PubMed id: 10089402 DOI: 10.1107/S090744499800938X

Date:

14-Mar-98 Release date: 05-Aug-98

Protein chains

No UniProt id for this chain

Struc: 214 a.a.

Protein chains

No UniProt id for this chain

Struc: 221 a.a.

DOI no: 10.1107/S090744499800938X

Acta Crystallogr D Biol Crystallogr 55:122-128 (1999)

PubMed id: 10089402

Structure of a monoclonal 2E8 Fab antibody fragment specific for the low-density lipoprotein-receptor binding region of apolipoprotein E refined at 1.9 A.

S.Trakhanov, S.Parkin, R.Raffaï, R.Milne, Y.M.Newhouse, K.H.Weisgraber, B.Rupp.

ABSTRACT

The crystal structure of the Fab fragment of 2E8, the monoclonal IgG1,kappa antibody specific for the low-density lipoprotein (LDL) receptor-binding region of apolipoprotein E (apoE), has been solved by molecular replacement and refined at 1.9 A resolution (PDB entry 12E8). Two 2E8 Fab molecules in the asymmetric unit are related by noncrystallographic symmetry and are hydrogen bonded through a beta-sheet-like intermolecular contact between the heavy-chain complementarity-determining regions 3 (CDRH3) of each molecule. The structure has been refined to an R value of 0.22 (Rfree = 0.27). The initially ill-defined heavy-chain constant domain (CH1) of 2E8 has been retraced with the aid of automatic refinement, confirming the beta-sheet tracing independently of any starting models. As a resolution better than 2 A is not common for Fab fragments, this model represents a well defined Fab structure and should prove useful in MR solution of other Fab fragments. Furthermore, in the absence of an LDL-receptor structure, the homology of the 2E8 CDRH2 to the ligand-binding domain of the LDL receptor has been exploited to model the apoE-LDL-receptor interaction.

Selected figure(s)

Figure 1.
Figure 1 Native Patterson map created by XtalView (McRee, 1992[McRee, D. E. (1992). J. Mol. Graph. 10, 44-46.]) showing the strong Harker peak indicative of an NCS axis parallel to the crystallographic 2[1] screw axis.

Figure 4.
Figure 4 Ribbon representation of the topology of the 2E8 Fab dimer. The two light chains (C[L] and V[L]) are red and yellow, respectively, and the two heavy chains (C[H1] and V[H]) are blue and green, respectively. The dimer interface is formed by the complementarity-determining regions. The figure was created with MOLSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.]).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1999, 55, 122-128) copyright 1999.

Figures were selected by the author.