PDBsum entry: 1nsn

Complex (immunoglobulin/hydrolase)

PDB id: 1nsn

Contents

Protein chains

217 a.a. *

210 a.a. *

138 a.a. *

* Residue conservation analysis

PDB id:

1nsn

Name:

Complex (immunoglobulin/hydrolase)

Title:

The crystal structure of antibody n10-staphylococcal nuclease complex at 2.9 angstroms resolution

Structure:

Igg fab (igg1, kappa). Chain: l. Synonym: n10 fab immunoglobulin. Igg fab (igg1, kappa). Chain: h. Synonym: n10 fab immunoglobulin. Staphylococcal nuclease. Chain: s. Synonym: staphylococcal nuclease ribonucleate,

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Strain: caf1. Staphylococcus aureus. Organism_taxid: 1280. Strain: foggi. Gene: nuclease. Expressed in: escherichia coli.

Biol. unit:

Trimer (from PQS)

Resolution:

2.80Å R-factor: 0.195

Authors:

S.Sheriff,P.Bossart-Whitaker

Key ref:

P.Bossart-Whitaker et al. (1995). The crystal structure of the antibody N10-staphylococcal nuclease complex at 2.9 A resolution. J Mol Biol, 253, 559-575. PubMed id: 7473734 DOI: 10.1006/jmbi.1995.0573

Date:

06-Jun-95 Release date: 15-Sep-95

Protein chain

No UniProt id for this chain

Protein chain

No UniProt id for this chain

Protein chain

P00644  (NUC_STAAU) -  Thermonuclease

Seq: 231 a.a.

Struc: 138 a.a.

Enzyme reactions

• Enzyme class: Chain S: E.C.3.1.31.1 - Micrococcal nuclease.
• Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotide end-products.

 Gene Ontology (GO) functional annotation 

• Biochemical function: nucleic acid binding (3 terms)

DOI no: 10.1006/jmbi.1995.0573

J Mol Biol 253:559-575 (1995)

PubMed id: 7473734

The crystal structure of the antibody N10-staphylococcal nuclease complex at 2.9 A resolution.

P.Bossart-Whitaker, C.Y.Chang, J.Novotny, D.C.Benjamin, S.Sheriff.

ABSTRACT

The three-dimensional structure of the antibody N10 Fab fragment complexed with staphylococcal nuclease (SNase) has been determined to 2.9 A resolution. Eighteen residues from six complementarity-determining regions (CDR) recognize an epitope of five distinct SNase segments with a total of 17 residues. The overall shape of the antibody-antigen interface is U-shaped rather than the more or less rectangular interface seen in other antibody-protein antigen interfaces. Despite the U-shaped interface, the amount of surface buried in the complex, 828 A2 for SNase and 793 A2 for N10, is typical of antibody-protein antigen complexes. Contributing to the shape of the interface is the shortest antibody heavy chain-CDR3 loop reported to date, which probably allows access of bulk solvent in the center of the "U" interface. Another unusual feature of the N10 antibody is the 15 residue antibody light chain-CDR1, a length seen in only three other reported antibodies. Antibody light chain-CDR1 displays a previously unobserved conformation in its distal portion. Finally, although some of the movement observed in the antibody-bound SNase may be due to crystal contacts, it is clear that some side-chain rearrangements are the result of antigen-antibody interaction.

Selected figure(s)

Figure 1.
Figure 1. Stereo diagram of the N10--SNase complex is shown as a ribbon structure. SNase is shown in cyan with the epitope contact residues in red. The N10 antibody heavy chain is in green and the light chain in yellow. For both heavy chain and light chain, the CDR regions are colored silver and the contact residues are in magenta. Figure produced with RIBBONS (Carson, 1991).

Figure 7.
Figure 7. Stereo diagram of the chain trace of CDR L1 of Fabs N10 (cyan), 40--50 (red), 50.1 (magenta), 59.1 (yellow). In addition, side-chains of N10 residues Phe L-30, Tyr L-32 and Trp L-92 are shown in cyan and canonical base residues (Ile L-2, Ala L-25, Val L-27B, Met L-33 and Phe L-71) are shown in dark blue. Figure produced with MOLSCRIPT (Kraulis, 1991) ``turn'' command so that tubes run through C a positions.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1995, 253, 559-575) copyright 1995.

Figures were selected by the author.