PITFALLS OF MOLECULAR REPLACEMENT - THE STRUCTURE DETERMINATION OF ANIMMUNOGLOBULIN LIGHT-CHAIN DIMER

Citation
Db. Huang et al., PITFALLS OF MOLECULAR REPLACEMENT - THE STRUCTURE DETERMINATION OF ANIMMUNOGLOBULIN LIGHT-CHAIN DIMER, Acta crystallographica. Section D, Biological crystallography, 52, 1996, pp. 1058-1066
Citations number
31
Language
INGLESE
art.tipo
Article
Categorie Soggetti
Crystallography,"Biochemical Research Methods",Biology
ISSN journal
0907-4449
Volume
52
Year of publication
1996
Part
6
Pages
1058 - 1066
Database
ISI
SICI code
0907-4449(1996)52:<1058:POMR-T>2.0.ZU;2-1
Abstract
The structure of protein Cle, a human light-chain dimer from the lambd a III subgroup, was determined using 2.6 Angstrom data; the R value is 18.4%. The structure was solved, after a false start, by molecular re placement with the lambda II/V Meg protein as a search structure. When the refinement did not proceed beyond an R value of 27%, it was disco vered that while the constant domains were in their correct positions in the unit cell, the incorrect variable domains were used for definin g the molecule. The correct solution required a rotation of 180 degree s around the local twofold axis that relates the two constant domains of the dimer. The correct variable domain positions overlap about 70% of the same volume as the incorrect ones of a symmetry-related molecul e. The refinement distorted the geometries of the domains. Though the constant domains were in their correct positions, the r.m.s. (root-mea n-square) deviation of the C alpha atom position was 1.2 Angstrom when the two constant domains were compared. For the correct structure, th is value is 0.5 Angstrom. The phi and psi angles, the r.m.s. chiral va lue and the free R value, even when calculated a posteriori, were good indicators of the correctness of the structure. The quaternary struct ure of the Cle molecule is similar to that in Meg (crystallized from a mmonium sulfate); the elbow bend is 115:. However, the arrangement of the variable domains differs from that observed in other variable doma in dimers. The variable domains of Cle are 0.7 Angstrom closer than in Meg or variable dimer Rei. The hydrogen bonding at the interface of t he two domains is novel. Residues Tyr36 from both monomers form a hydr ogen bond that is part of a network with the Gln89 residues from both monomers. For the first time hydrogen bonds were observed between the main-chain peptide N and O atoms of the complementarity-determining re gion CDR2 and CDR3 segments of both monomers.