PDBsum entry 1kcr

Immune system

PDB id: 1kcr

Contents

Protein chains

213 a.a. *

218 a.a. *

15 a.a. *

Waters ×31

* Residue conservation analysis

PDB id:

1kcr

Name:

Immune system

Title:

Crystal structure of antibody pc283 in complex with ps1 peptide

Structure:

Pc283 immunoglobulin. Chain: l. Fragment: light chain. Pc283 immunoglobulin. Chain: h. Fragment: heavy chain. Ps1 peptide. Chain: p. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Synthetic: yes. Other_details: the peptide was chemically synthesized. The sequence of the peptide is naturally found in hepatitis b virus.

Biol. unit:

Trimer (from PQS)

Resolution:

2.90Å R-factor: 0.184 R-free: 0.277

Authors:

D.T.Nair,K.Singh,N.Sahu,K.V.S.Rao,D.M.Salunke

Key ref:

D.T.Nair et al. (2000). Crystal structure of an antibody bound to an immunodominant peptide epitope: novel features in peptide-antibody recognition. J Immunol, 165, 6949-6955. PubMed id: 11120821

Date:

11-Nov-01 Release date: 11-May-02

Protein chain

P01837  (IGKC_MOUSE) -  Immunoglobulin kappa constant from Mus musculus

Seq: 107 a.a.

Struc: 213 a.a.*

Protein chain

P01869  (IGH1M_MOUSE) -  Ig gamma-1 chain C region, membrane-bound form from Mus musculus

Seq: 393 a.a.

Struc: 218 a.a.*

Protein chain

Q91C35  (HBSAG_HBVA6) -  Large envelope protein from Hepatitis B virus genotype A1 subtype adw2 (isolate South Africa/84/2001)

Seq: 389 a.a.

Struc: 15 a.a.

* PDB and UniProt seqs differ at 11 residue positions (black crosses)

J Immunol 165:6949-6955 (2000)

PubMed id: 11120821

Crystal structure of an antibody bound to an immunodominant peptide epitope: novel features in peptide-antibody recognition.

D.T.Nair, K.Singh, N.Sahu, K.V.Rao, D.M.Salunke.

ABSTRACT

The crystal structure of Fab of an Ab PC283 complexed with its corresponding peptide Ag, PS1 (HQLDPAFGANSTNPD), derived from the hepatitis B virus surface Ag was determined. The PS1 stretch Gln2P to Phe7P is present in the Ag binding site of the Ab, while the next three residues of the peptide are raised above the binding groove. The residues Ser11P, Thr12P, and Asn13P then loop back onto the Ag-binding site of the Ab. The last two residues, Pro14P and Asp15P, extend outside the binding site without forming any contacts with the Ab. The PC283-PS1 complex is among the few examples where the light chain complementarity-determining regions show more interactions than the heavy chain complementarity-determining regions, and a distal framework residue is involved in Ag binding. As seen from the crystal structure, most of the contacts between peptide and Ab are through the five residues, Leu3-Asp4-Pro5-Ala6-Phe7, of PS1. The paratope is predominantly hydrophobic with aromatic residues lining the binding pocket, although a salt bridge also contributes to stabilizing the Ag-Ab interaction. The molecular surface area buried upon PS1 binding is 756 A(2) for the peptide and 625 A(2) for the Fab, which is higher than what has been seen to date for Ab-peptide complexes. A comparison between PC283 structure and a homology model of its germline ancestor suggests that paratope optimization for PS1 occurs by improving both charge and shape complementarity.