title: Structure of a single-chain antibody variable domain (Fv) fragment complexed with a carbohydrate antigen at 1.7-A resolution.
abstract: We describe here the 1.7-A resolution structure of a single-chain antibody variable domain (scFv) molecule, based on the carbohydrate-binding antibody Se155-4, complexed with the trisaccharide ligand alpha-D-Gal(1-->2)[alpha-D-Abe(1-->3)]alpha-D-Manp1-->OMe, where Abe is abequose. The scFv expressed in Escherichia coli has the variable region light chain to heavy chain polarity with the domains connected by a 19-residue linker. Although the linker is partially disordered in the crystal, the packing of the molecules suggests a monomeric state of the scFv. The carbohydrate adopts a different conformation about the Man-Gal linkage than was observed previously in the Fab-trisaccharide complex. Instead of a direct hydrogen bond between O2Abe and O2Gal, these two atoms are bridged by a water molecule in the present complex.
authors.affiliation: Biotechnology Research Institute, National Research Council of Canada, Montreal, PQ.
authors.forename: A
authors.initials: A
authors.lastname: Zdanov
authors.forename: Y
authors.initials: Y
authors.lastname: Li
authors.forename: D R
authors.initials: DR
authors.lastname: Bundle
authors.forename: S J
authors.initials: SJ
authors.lastname: Deng
authors.forename: C R
authors.initials: CR
authors.lastname: MacKenzie
authors.forename: S A
authors.initials: SA
authors.lastname: Narang
authors.forename: N M
authors.initials: NM
authors.lastname: Young
authors.forename: M
authors.initials: M
authors.lastname: Cygler
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001425:Bacterial Outer Membrane Proteins / Q000235:genetics; D002236:Carbohydrate Conformation; D002240:Carbohydrate Sequence; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray / Q000379:methods; D000939:Epitopes / Q000378:metabolism; D004926:Escherichia coli; D005803:Genes, Immunoglobulin; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry; D007074:Immunoglobulin G / Q000737:chemistry*; D007135:Immunoglobulin Variable Region / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008070:Lipopolysaccharides / Q000276:immunology; D051379:Mice; D008969:Molecular Sequence Data; D009844:Oligosaccharides / Q000378:metabolism*; D011487:Protein Conformation; D011993:Recombinant Fusion Proteins / Q000096:biosynthesis / Q000737:chemistry; D012475:Salmonella / Q000276:immunology
chemical_list: D001425:Bacterial Outer Membrane Proteins; D000939:Epitopes; D007140:Immunoglobulin Fab Fragments; D007074:Immunoglobulin G; D007135:Immunoglobulin Variable Region; D008070:Lipopolysaccharides; D009844:Oligosaccharides; D011993:Recombinant Fusion Proteins