1MAK

SOLUTION STRUCTURE OF AN ISOLATED ANTIBODY VL DOMAIN


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 15 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Solution structure of an isolated antibody VL domain.

Constantine, K.L.Friedrichs, M.S.Metzler, W.J.Wittekind, M.Hensley, P.Mueller, L.

(1994) J.Mol.Biol. 236: 310-327

  • DOI: 10.1006/jmbi.1994.1137
  • Primary Citation of Related Structures:  1MAJ

  • PubMed Abstract: 
  • The solution structure of the isolated VL domain of the anti-digoxin antibody 26-10 has been determined using data derived from heteronuclear multi-dimensional nuclear magnetic resonance (n.m.r.) experiments. Analytical ultracentrifugation and n.m.r. ...

    The solution structure of the isolated VL domain of the anti-digoxin antibody 26-10 has been determined using data derived from heteronuclear multi-dimensional nuclear magnetic resonance (n.m.r.) experiments. Analytical ultracentrifugation and n.m.r. data demonstrate that the VL domain is only weakly associating (Kd = 2.5 (+/- 0.7) mM) and that it experiences a rapid monomer/dimer equilibrium under the n.m.r. experimental conditions. Therefore, the results reported here represent the first structure determination of an antibody VL domain in the absence of fixed quaternary interactions. The structure determination is based on 930 proton-proton distance constraints, 113 dihedral angle constraints, and 46 hydrogen bond constraints. Eighty initial structures were calculated with the variable target function program DIANA; of these, 31 were accepted on the basis of satisfaction of constraints (no distance constraint violations > 0.5 A; target function < 3.0 A2). Accepted DIANA structures were refined by restrained energy minimization using the X-PLOR program. The 15 best energy-minimized DIANA structures were chosen as a representative ensemble of solution conformations. The average root-mean-square differences (r.m.s.d.) between the individual structures of this ensemble and the mean coordinates is 0.85 (+/- 0.10) A for all backbone atoms and 1.29 (+/- 0.10) A for all heavy atoms. For beta-strands A, B, C, D, E and F, the average backbone atom r.m.s.d. to the mean structure is 0.46 (+/- 0.06) A. A higher-resolution ensemble, with all backbone atom and all heavy atom r.m.s.d.s. to the mean coordinates of 0.54 (+/- 0.08) A and 0.98 (+/- 0.12) A, respectively, was obtained by X-PLOR simulated annealing refinement of the 15 energy-minimized DIANA structures. A detailed analysis of the original ensemble of 15 energy-minimized DIANA structures is presented, as this ensemble retains a broader, and possibly more realistic, sampling of conformation space. The backbone atom and all heavy atom r.m.s.d.s between the mean energy-minimized DIANA structure and the X-ray derived coordinates of the VL domain within the Fab/digoxin complex are 1.05 A and 1.56 A, respectively. Subtle differences between the solution and X-ray structures occur primarily in CDR2, CDR3, beta-strands A, F and G, and localized regions of hydrophobic packing. Overall, these results demonstrate that the 26-10 VL domain conformation is determined primarily by intradomain interactions, and that quaternary VL-VH association induces relatively minor conformational adjustments.


    Related Citations: 
    • Production and Characterization of an Antibody Fv Fragment 15N-Labelled in the Vl Domain Only
      Goldfarb, V.,Wittekind, M.,Jeffrey, P.D.,Mueller, L.,Constantine, K.L.
      (1993) J.Mol.Biol. 232: 15
    • Sequential 1H and 15N NMR Assignments and Secondary Structure of a Recombinant Anti-Digoxin Antibody Vl Domain
      Constantine, K.L.,Goldfarb, V.,Wittekind, M.,Anthony, J.,Ng, S.-C.,Mueller, L.
      (1992) Biochemistry 31: 5033
    • Characterization of the Backbone Dynamics of an Anti-Digoxin Antibody Vl Domain by Inverse Detected 1H-15N NMR: Comparisons with X-Ray Data for the Fab
      Constantine, K.L.,Friedrichs, M.S.,Goldfarb, V.,Jeffrey, P.D.,Sheriff, S.,Mueller, L.
      (1993) Proteins 15: 290
    • 26-10 Fab: Digoxin Complex-Affinity and Specificity from Surface Complementarity
      Jeffrey, P.D.,Strong, R.K.,Sieker, L.C.,Chang, C.Y.,Campbell, R.L.,Petsko, G.A.,Haber, E.,Margolies, M.N.,Sheriff, S.
      () TO BE PUBLISHED --: --
    • Aliphatic 1H and 13C Resonance Assignments for the 26-10 Antibody Vl Domain Derived from Heteronuclear Multidimensional NMR Spectroscopy
      Constantine, K.L.,Goldfarb, V.,Wittekind, M.,Friedrichs, M.S.,Anthony, J.,Ng, S.-C.,Mueller, L.
      (1993) J.Biomol.NMR 3: 41


    Organizational Affiliation

    Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, NJ 08543.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGG2A-KAPPA 26-10 FV (LIGHT CHAIN)
A
113Mus musculusN/A
Find proteins for P01631 (Mus musculus)
Go to UniProtKB:  P01631
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 15 
  • Olderado: 1MAK Olderado
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other