IMGT Web resources: IMGT repertoire

Collier de Perles: Mouse (Mus musculus) IGH V-D-J REGION from E5.2 Fv (PDB: 1dvf_D)

IMGT/3Dstructure-DB card: 1dvf

Side view (backbone model)
View from above the CDRs (backbone model)

Mouse rearranged IGH V-D-J2 REGION (with IMGT modification)

[8.8.15]

The PBD file 1dvf contains the atomic coordinates of the complex between Idiotope D1.3-Antiidiotope E5.2. Both D1.3 and E5.2 are mouse (Mus musculus) antibodies (IgG1, kappa). Only the IGH V-DOMAIN of E5.2 "Fv" (for "Fragment variable") (PDB: 1dvf_D) is displayed here.

IMGT modification:

IMGT unique numbering for the graphical representation of the IGH V-D-J REGION of the mouse antibody E5.2 Fv revealed a conflict between the amino acid sequence and the atomic coordinate data, in the PDB file 1dvf: Leu-Ser-Leu (SEQRES lines) and Leu-Leu-Leu (ATOM lines). The original sequence [1] is Leu-Ser-Ser-Leu (positions 91 to 94 in the IMGT unique numbering; the Serine added at position 93 is shown between parentheses).
[1] Goldbaum F.A. et al., J. Mol. Biol., 241, 739 (1994)

Legend:

Amino acids are shown in the one-letter abbreviation.
Hydrophobic amino acids (hydropathy index with positive value) and Tryptophan (W) found at a given position in more than 50 % of analysed Ig and TcR sequences are shown in blue.
All Proline (P) are shown in yellow.
The CDR-IMGT are limited by amino acids shown in squares, which belong to the neighbouring FR-IMGT. The CDR3-IMGT is described using the IMGT unique numbering for V-DOMAIN.
Hatched circles or squares correspond to missing positions according to the IMGT unique numbering for V-REGIONs. Missing positions of the CDRs are not shown in this representation.
Arrows indicate the direction of the beta strands and their different designations in 3D structure.

Created: 19/12/1997
Last updated: Friday, 22-Sep-2023 18:17:01 CEST
Authors: Manuel Ruiz, Elodie Foulquier and Marie-Paule Lefranc
Editors: Elodie Foulquier and Marie-Paule Lefranc