PDBsum entry 1f11

Immune system

PDB id: 1f11

Contents

Protein chains

216 a.a. *

218 a.a. *

* Residue conservation analysis

PDB id:

1f11

Name:

Immune system

Title:

F124 fab fragment from a monoclonal anti-pres2 antibody

Structure:

F124 immunoglobulin (kappa light chain). Chain: a, c. Fragment: fab fragment (unp p01665 residues 1-111, p01837 residues 1- 106). F124 immunoglobulin (igg1 heavy chain). Chain: b, d. Fragment: fab fragment (unp q65zr6 residues 18-134, p01869 residues 2-102)

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Organism_taxid: 10090

Biol. unit:

Dimer (from PQS)

Resolution:

3.00Å R-factor: 0.184 R-free: 0.271

Authors:

F.A.Saul,B.Vulliez-Le Normand,M.Passafiume,M.M.Riottot,G.A.Bentley

Key ref:

F.A.Saul et al. (2000). Structure of the Fab fragment from F124, a monoclonal antibody specific for hepatitis B surface antigen. Acta Crystallogr D Biol Crystallogr, 56, 945-951. PubMed id: 10944330 DOI: 10.1107/S0907444900008088

Date:

18-May-00 Release date: 30-Aug-00

Protein chains

P01665  (KV3AD_MOUSE) -  Ig kappa chain V-III region PC 7043 from Mus musculus

Seq: 111 a.a.

Struc: 216 a.a.*

Protein chains

P01837  (IGKC_MOUSE) -  Immunoglobulin kappa constant from Mus musculus

Seq: 107 a.a.

Struc: 216 a.a.

Protein chains

Q9D8L4  (Q9D8L4_MOUSE) -  Ig-like domain-containing protein from Mus musculus

Seq: 473 a.a.

Struc: 218 a.a.*

* PDB and UniProt seqs differ at 47 residue positions (black crosses)

DOI no: 10.1107/S0907444900008088

Acta Crystallogr D Biol Crystallogr 56:945-951 (2000)

PubMed id: 10944330

Structure of the Fab fragment from F124, a monoclonal antibody specific for hepatitis B surface antigen.

F.A.Saul, B.Vulliez-Le Normand, M.Passafiume, M.M.Riottot, G.A.Bentley.

ABSTRACT

The crystal structure of the Fab fragment from the monoclonal anti-preS2 antibody F124 (IgG1,kappa) has been solved by molecular replacement and refined at 3.0 A resolution. The Fab crystallizes with two independent molecules in the asymmetric unit. F124 recognizes an epitope contained within the preS2 segment between residues 120 and 132 of the surface antigen of hepatitis B virus. The antibody shows a high affinity for the glycan N-linked to Asn123, but it also cross-reacts with the non-glycosylated peptide fragment 120-132. Although crystallization was performed in the presence of an eightfold excess of the cross-reactive peptide, no evidence for the ligand was found in the antigen-binding site, which is close to a neighbouring molecule in the crystal lattice. The antigen-binding site has a groove-like topology which is modulated with pocket-like cavities. It is characterized by a large number of tyrosine and aspartate residues. The importance of germ-line mutations at the binding site is discussed.

Selected figure(s)

Figure 1.
Figure 1 Ramachandran plot for the two independent molecules of Fab F124. A total of 83.6% of the non-glycine residues fall in the most favoured regions and 15.6% in the additional allowed region. AlaL51, which is in an unfavoured region, has dihedral angles that are characteristic of a -turn (Milner-White et al., 1988[Milner-White, E. J., Ross, B. M., Ismail, R., Belhady-Mostefa, K. & Poet, R. (1988). J. Mol. Biol. 204, 777-782.]). Residues in the unfavoured regions are labelled; glycines are shown as triangles. (Produced by the program PROCHECK; Laskowski et al., 1993 [Laskowski, R. A., McArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). J. Appl. Cryst.

Figure 5.
Figure 5 A stereoview of the antigen-binding site colour-coded for electrostatic potential; red represents positive and blue negative. (Prepared with the program GRASP; Nicholls et al., 1991[Nicholls, A., Sharp, K. A. & Honig, B. (1991). Proteins Struct. Funct. Genet. 11, 281-296.].)

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2000, 56, 945-951) copyright 2000.

Figures were selected by an automated process.