PDBsum entry 1seq

Immune system

PDB id: 1seq

Contents

Protein chains

208 a.a. *

221 a.a. *

Ligands

TRS

IPA

SO4 ×4

Waters ×351

* Residue conservation analysis

PDB id:

1seq

Name:

Immune system

Title:

Fab mnac13

Structure:

Monoclonal antibody mnac13. Chain: l. Fragment: fab light chain. Monoclonal antibody mnac13. Chain: h. Fragment: fab heavy chain

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Other_details: hybridoma. Other_details: hybridoma

Biol. unit:

Dimer (from PQS)

Resolution:

1.78Å R-factor: 0.194 R-free: 0.232

Authors:

S.Covaceuszach,A.Cattaneo,D.Lamba

Key ref:

S.Covaceuszach et al. (2005). Neutralization of NGF-TrkA receptor interaction by the novel antagonistic anti-TrkA monoclonal antibody MNAC13: a structural insight. Proteins, 58, 717-727. PubMed id: 15625712 DOI: 10.1002/prot.20366

Date:

18-Feb-04 Release date: 01-Mar-05

Protein chain

P01837  (IGKC_MOUSE) -  Immunoglobulin kappa constant from Mus musculus

Seq: 107 a.a.

Struc: 208 a.a.*

Protein chain

P01868  (IGHG1_MOUSE) -  Ig gamma-1 chain C region secreted form from Mus musculus

Seq: 324 a.a.

Struc: 221 a.a.*

* PDB and UniProt seqs differ at 9 residue positions (black crosses)

DOI no: 10.1002/prot.20366

Proteins 58:717-727 (2005)

PubMed id: 15625712

Neutralization of NGF-TrkA receptor interaction by the novel antagonistic anti-TrkA monoclonal antibody MNAC13: a structural insight.

S.Covaceuszach, A.Cattaneo, D.Lamba.

ABSTRACT

MNAC13, a mouse monoclonal antibody, recognizes with high affinity and specificity the neurotrophin receptor TrkA and displays a neutralizing activity toward the NGF/TrkA interaction. Detailed knowledge of the molecular basis determining the specificity of this antibody is of importance because of its potential use as a modulator of the TrkA-mediated NGF activity. Here, we report a full biochemical and structural characterization of the MNAC13 antibody. Epitope mapping studies, by serial deletion mutants and by phage display, reveal a conformational epitope that is localized on the carboxy-terminal region of the first immunoglobulin-like domain (d4) of TrkA. The X-ray crystal structure of the MNAC13 Fab fragment has been determined and refined to 1.8 A resolution. The antigen-binding site is characterized by a crevice, surrounded by hydrophilic-charged residues on either side, dipping deep toward three mainly hydrophobic subsites. Remarkably an isopropanol molecule has been found to bind in one of the hydrophobic crevices. Overall, the surface topology (shape and electrostatic potential) of the combining site is consistent with the binding data on TrkA ECD serial deletions mutants. The structure of the MNAC13 Fab fragment may assist in the rational structure-based design of high affinity humanized forms of MNAC13, appropriate for therapeutic approaches in neuropathy and inflammatory pain states.

Selected figure(s)

Figure 2.
Figure 2. Perspective view of FabMNAC13 binding site: A: Hydrophobic and hydrophilic characteristics of the antigen-bindingsite of MNAC13 Fab fragment: (hydrophilic residues are colored in cyan, hydrophobic residues in green, basic residues in blue and acidic residues in red): molecular surface representation of FabMNAC13 P1 pocket with bound isopropanol colored in yellow (right) and empty (left). Figures produced by GRASP.[56] B: Stereo view of the cleft with the final [a] weighted 2Fo-Fc map contoured at 1.5 ; showing an isopropanol molecule (green density) and a water molecule trapped at the bottom of the P1 subsite encompassing Tyr L32, Trp L91 and His L34 (blue density).

Figure 3.
Figure 3. Homology structure-based TrkA d4 domain model to telokin[35] (PDBID 1FHG) template produced with the 3D-PSSm server,[34] MNAC13 epitope is shown in red: (A) Sequence alignment of TrkA_d4 with the two templates, (B) Ribbon representation of TrkA d4 model.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 58, 717-727) copyright 2005.

Figures were selected by an automated process.