PDBsum entry 2orb

Immune system

PDB id: 2orb

Contents

Protein chains

212 a.a. *

212 a.a. *

Ligands

SO4 ×2

Waters ×257

* Residue conservation analysis

PDB id:

2orb

Name:

Immune system

Title:

The structure of the anti-c-myc antibody 9e10 fab fragment

Structure:

Monoclonal anti-c-myc antibody 9e10. Chain: l, m. Fragment: light chain of antigen binding fragment, fab. Monoclonal anti-c-myc antibody 9e10. Chain: h, i. Fragment: heavy chain of antigen binding fragment, fab

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Strain: balb/c. Strain: balb/c

Resolution:

2.20Å R-factor: 0.261 R-free: 0.317

Authors:

N.Krauss,P.Scheerer,W.Hoehne

Key ref:

N.Krauss et al. (2008). The structure of the anti-c-myc antibody 9E10 Fab fragment/epitope peptide complex reveals a novel binding mode dominated by the heavy chain hypervariable loops. Proteins, 73, 552-565. PubMed id: 18473392 DOI: 10.1002/prot.22080

Date:

02-Feb-07 Release date: 12-Feb-08

Protein chains

No UniProt id for this chain

Struc: 212 a.a.

Protein chains

No UniProt id for this chain

Struc: 212 a.a.

DOI no: 10.1002/prot.22080

Proteins 73:552-565 (2008)

PubMed id: 18473392

The structure of the anti-c-myc antibody 9E10 Fab fragment/epitope peptide complex reveals a novel binding mode dominated by the heavy chain hypervariable loops.

N.Krauss, H.Wessner, K.Welfle, H.Welfle, C.Scholz, M.Seifert, K.Zubow, J.Aÿ, M.Hahn, P.Scheerer, A.Skerra, W.Höhne.

ABSTRACT

The X-ray structure of the Fab fragment from the anti-c-myc antibody 9E10 was determined both as complex with its epitope peptide and for the free Fab. In the complex, two Fab molecules adopt an unusual head to head orientation with the epitope peptide arranged between them. In contrast, the free Fab forms a dimer with different orientation. In the Fab/peptide complex the peptide is bound to one of the two Fabs at the "back" of its extended CDR H3, in a cleft with CDR H1, thus forming a short, three-stranded antiparallel beta-sheet. The N- and C-terminal parts of the peptide are also in contact with the neighboring Fab fragment. Comparison between the CDR H3s of the two Fab molecules in complex with the peptide and those from the free Fab reveals high flexibility of this loop. This structural feature is in line with thermodynamic data from isothermic titration calorimetry.

Selected figure(s)

Figure 2.
Figure 2. Superposition of antibody 9E10 C[ ]traces (variable domains) in stereo representation. (A) The epitope peptide complex for Fab(a) (V[L]: blue; V[H]: yellow; epitope peptide: red sticks) and Fab(b) (V[L]: light blue; V[H]: orange). Only the framework C[ ]coordinates were used for superposition, yielding an rmsd of 0.92 Å. (B) Fab(a) from the complex (light chain: blue; heavy chain fragment: yellow; epitope peptide: red sticks) and free Fab(a) (light chain: light blue; heavy chain fragment: orange, rmsd 0.45 Å for framework C[ ]positions).

Figure 6.
Figure 6. Topology of three-stranded -sheet formed between the epitope peptide and CDR H3. (A) in Fab 9E10, (B) Fab 447-52D, shown as ribbon representations. Orientations and color codings are the same as in Figure 5(B).

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 73, 552-565) copyright 2008.

Figures were selected by an automated process.