2·9 Å resolution structure of an anti-dinitrophenyl-spin-label monoclonal antibody Fab fragment with bound hapten

Axel T. Brünger, Daniel J. Leahy, Thomas R. Hynes, Robert O. Fox

Research output: Contribution to journalArticlepeer-review

Abstract

The crystal structure of the Fab fragment of the murine monoclonal anti-dinitrophenyl-spin-label antibody AN02 complexed with its hapten has been solved at 2·9 Å resolution using a novel molecular replacement method. Prior to translation searches, a large number of the most likely rotation function solutions were subjected to a rigid body refinement against the linear correlation coefficient between intensities of observed and calculated structure factors. First, the overall orientation of the search model and then the orientations and positions of the four Fab domains (VH, VL, CH1 and CL) were refined. This procedure clearly identified the correct orientation of the search model. The refined search model was then subjected to translation searches which unambiguously determined the enantiomer and position in the unit cell of the crystal. The successful search model was the refined 2·5 Å crystal structure of the Fab fragment of HyHel-5 from which non-matching residues in the variable domains had been removed. HyHel-5 is a murine monoclonal antibody whose heavy and light chains are of the same subclass (γ1, κ, respectively) as AN02. After molecular replacement the structure of the AN02 Fab has been refined using simulated annealing in combination with model building and conjugate gradient refinement to a current crystallographic R-factor of 19·5% for 12,129 unique reflections between 8·0 and 2·9 Å. The root-mean-square (r.m.s.) deviation from ideal bond lengths is 0·014 Å, and the r.m.s. deviation from ideal bond angles is 3·1°. The electron density reveals the hapten sitting in a pocket formed by the loops of the complementarity determining region. The dinitrophenyl ring of the hapten is sandwiched between the indole rings of Trp96 of the heavy-chain and Trp91 of the light-chain. The positioning of the hapten and general features of the combining site are in good agreement with the results of earlier nuclear magnetic resonance experiments.

Original languageEnglish (US)
Pages (from-to)239-256
Number of pages18
JournalJournal of molecular biology
Volume221
Issue number1
DOIs
StatePublished - Sep 5 1991

Keywords

  • PC-refinement
  • antibody
  • crystal structure
  • fab fragment
  • molecular replacement

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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