1ngp: Difference between revisions

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N1G9 (IGG1-LAMBDA) FAB FRAGMENT COMPLEXED WITH (4-HYDROXY-3-NITROPHENYL) ACETATE

OverviewOverview

The three-dimensional structures of the Fab fragment, in its unliganded and liganded crystals, of mouse anti-(4-hydroxy-3-nitrophenyl)acetate (NP) antibody N1G9 have been determined by the molecular replacement method. The unliganded and NP-liganded structures were refined at 2.4 A resolution to crystallographic R-factors of 0.194 and 0.196, respectively. Antibody N1G9 bears lambda light chains, and is one of the primary immune response antibodies. Fab N1G9 exhibits an elbow angle of 197 degrees in both structures. This large angle is ascribed to the VL-CL interface formed by lambda-chain residues. A hydrophobic pocket surrounded by the complementarity-determining regions except L2 is identified as a hapten-binding site. Between the liganded and unliganded structures, root-mean-square (r.m.s.) positional deviations are 0.42 A for the main-chain atoms, and 0.74 A for all the protein atoms. The major structural differences between these structures are localized in the hapten-binding site, and yield an r.m.s. deviation of 1.03 A for the side-chain atoms. The soaked NP ligand is in van der Waals contact with the aromatic side-chains of Tyr32L and Trp91L of the light chain, and Trp33H and Tyr97H of the heavy chain, and is hydrogen-bonded to the side-chains of Trp96L, His35H, Arg50H, Tyr95H, and Ser100aH. The side-chain of Lys58H is salt-bridged to the NP hydroxyl group. The side-chains of Arg50H, Trp33H, and Tyr97H are shifted toward the NP carboxyl group. The side-chain of Trp33H, whose replacement to Leu increases affinity by tenfold, is sandwiched between the Arg50H and Tyr97H side-chains, and is in cramped contact both with the ligand and with these side-chains. Affinity increases in the maturation of the anti-NP antibodies are ascribable to conformational relief of these cramped contacts through the replacement of Trp33H or through suitable structural alterations in the H3 region.

About this StructureAbout this Structure

1NGP is a Protein complex structure of sequences from Mus musculus with and as ligands. Full crystallographic information is available from OCA.

ReferenceReference

Three-dimensional structures of the Fab fragment of murine N1G9 antibody from the primary immune response and of its complex with (4-hydroxy-3-nitrophenyl)acetate., Mizutani R, Miura K, Nakayama T, Shimada I, Arata Y, Satow Y, J Mol Biol. 1995 Nov 24;254(2):208-22. PMID:7490744

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 '''N1G9 (IGG1-LAMBDA) FAB FRAGMENT COMPLEXED WITH (4-HYDROXY-3-NITROPHENYL) ACETATE'''<br />
 ==Overview==
-The three-dimensional structures of the Fab fragment, in its unliganded, and liganded crystals, of mouse anti-(4-hydroxy-3-nitrophenyl)acetate (NP), antibody N1G9 have been determined by the molecular replacement method., The unliganded and NP-liganded structures were refined at 2.4 A resolution, to crystallographic R-factors of 0.194 and 0.196, respectively. Antibody, N1G9 bears lambda light chains, and is one of the primary immune response, antibodies. Fab N1G9 exhibits an elbow angle of 197 degrees in both, structures. This large angle is ascribed to the VL-CL interface formed by, lambda-chain residues. A hydrophobic pocket surrounded by the, complementarity-determining regions except L2 is identified as a, hapten-binding site. Between the liganded and unliganded structures, root-mean-square (r.m.s.) positional deviations are 0.42 A for the, main-chain atoms, and 0.74 A for all the protein atoms. The major, structural differences between these structures are localized in the, hapten-binding site, and yield an r.m.s. deviation of 1.03 A for the, side-chain atoms. The soaked NP ligand is in van der Waals contact with, the aromatic side-chains of Tyr32L and Trp91L of the light chain, and, Trp33H and Tyr97H of the heavy chain, and is hydrogen-bonded to the, side-chains of Trp96L, His35H, Arg50H, Tyr95H, and Ser100aH. The, side-chain of Lys58H is salt-bridged to the NP hydroxyl group. The, side-chains of Arg50H, Trp33H, and Tyr97H are shifted toward the NP, carboxyl group. The side-chain of Trp33H, whose replacement to Leu, increases affinity by tenfold, is sandwiched between the Arg50H and Tyr97H, side-chains, and is in cramped contact both with the ligand and with these, side-chains. Affinity increases in the maturation of the anti-NP, antibodies are ascribable to conformational relief of these cramped, contacts through the replacement of Trp33H or through suitable structural, alterations in the H3 region.
+The three-dimensional structures of the Fab fragment, in its unliganded and liganded crystals, of mouse anti-(4-hydroxy-3-nitrophenyl)acetate (NP) antibody N1G9 have been determined by the molecular replacement method. The unliganded and NP-liganded structures were refined at 2.4 A resolution to crystallographic R-factors of 0.194 and 0.196, respectively. Antibody N1G9 bears lambda light chains, and is one of the primary immune response antibodies. Fab N1G9 exhibits an elbow angle of 197 degrees in both structures. This large angle is ascribed to the VL-CL interface formed by lambda-chain residues. A hydrophobic pocket surrounded by the complementarity-determining regions except L2 is identified as a hapten-binding site. Between the liganded and unliganded structures, root-mean-square (r.m.s.) positional deviations are 0.42 A for the main-chain atoms, and 0.74 A for all the protein atoms. The major structural differences between these structures are localized in the hapten-binding site, and yield an r.m.s. deviation of 1.03 A for the side-chain atoms. The soaked NP ligand is in van der Waals contact with the aromatic side-chains of Tyr32L and Trp91L of the light chain, and Trp33H and Tyr97H of the heavy chain, and is hydrogen-bonded to the side-chains of Trp96L, His35H, Arg50H, Tyr95H, and Ser100aH. The side-chain of Lys58H is salt-bridged to the NP hydroxyl group. The side-chains of Arg50H, Trp33H, and Tyr97H are shifted toward the NP carboxyl group. The side-chain of Trp33H, whose replacement to Leu increases affinity by tenfold, is sandwiched between the Arg50H and Tyr97H side-chains, and is in cramped contact both with the ligand and with these side-chains. Affinity increases in the maturation of the anti-NP antibodies are ascribable to conformational relief of these cramped contacts through the replacement of Trp33H or through suitable structural alterations in the H3 region.
 ==About this Structure==
-NGP is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with SO4 and NPA as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NGP OCA].
+NGP is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=NPA:'>NPA</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NGP OCA].
 ==Reference==
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 [[Category: immunoglobulin]]
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