 |
PDBsum entry 1ngq
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Immunoglobulin
|
PDB id
|
|
|
|
1ngq
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
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.
|
|
|
Authors
|
|
R.Mizutani,
K.Miura,
T.Nakayama,
I.Shimada,
Y.Arata,
Y.Satow.
|
|
|
Ref.
|
|
J Mol Biol, 1995,
254,
208-222.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
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.
|
|
|
|
|
|
|
|
Figure 2.
Figure 2. Fourier maps for the unliganded N1G9 Fab crystal. (a) The 2Fo - Fc map is shown for the vicinity of Arg50H,
contoured at 1.5s level. (b) The 2Fo - Fc difference Fourier map shown for the vicinity of Trp200H, whose side-chain
N
e1
atom forms two hydrogen bonds (shown by the broken lines) with a water molecule (indicated by a cross) and with
the carbonyl O of Ile223H. For the preparation of panel b, the side-chain of Trp200H was omitted from the unliganded
structure, and then the structure was refined with X-PLOR. The phases and amplitudes thus obtained were used in
the calculation of the 2Fo - Fc difference Fourier map, contoured at 1.2s level. The Figures were produced using
Turbo-FRODO (Roussel & Cambillau, 1991). The structural models labeled with sequence numbers are superimposed
on the maps.
|
|
Figure 7.
Figure 7. Stereo drawing of the
VL--CL interface of the N1G9 Fab.
Some residues are labeled with their
sequence numbers. The VL--CL joint
formed by hydrophobic residues
Thr12L, Thr105L, Leu106aL,
Tyr140L, and Pro141L is character-
istic for the l chains. The Figure was
produced using PLUTO (Mother-
well & Clegg, 1978).
|
|
|
|
|
|
The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1995,
254,
208-222)
copyright 1995.
|
|
|
Secondary reference #1
|
|
|
Title
|
|
Antibody engineering for the analysis of affinity maturation of an anti-Hapten response.
|
|
|
Authors
|
|
D.Allen,
T.Simon,
F.Sablitzky,
K.Rajewsky,
A.Cumano.
|
|
|
Ref.
|
|
Embo J, 1988,
7,
1995-2001.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #2
|
|
|
Title
|
|
Structure of primary anti-(4-Hydroxy-3-Nitrophenyl)acetyl (np) antibodies in normal and idiotypically suppressed c57bl/6 mice.
|
|
|
Authors
|
|
A.Cumano,
K.Rajewsky.
|
|
|
Ref.
|
|
Eur J Immunol, 1985,
15,
512-520.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #3
|
|
|
Title
|
|
Somatic variants of murine immunoglobulin lambda light chains.
|
|
|
Authors
|
|
A.L.Bothwell,
M.Paskind,
M.Reth,
T.Imanishi-Kari,
K.Rajewsky,
D.Baltimore.
|
|
|
Ref.
|
|
Nature, 1982,
298,
380-382.
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
|
