|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
J Mol Biol
254:208-222
(1995)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
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.
|
|
R.Mizutani,
K.Miura,
T.Nakayama,
I.Shimada,
Y.Arata,
Y.Satow.
|
|
|
|
|
| |
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.
|
|
|
|
|
|
| |
Selected figure(s)
|
|
|
|
| |
|
|
|
|
|
|
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.
|
|
| |
Figures were
selected
by an automated process.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
C.M.Radcliffe,
J.N.Arnold,
D.M.Suter,
M.R.Wormald,
D.J.Harvey,
L.Royle,
Y.Mimura,
Y.Kimura,
R.B.Sim,
S.Inogès,
M.Rodriguez-Calvillo,
N.Zabalegui,
A.L.de Cerio,
K.N.Potter,
C.I.Mockridge,
R.A.Dwek,
M.Bendandi,
P.M.Rudd,
and
F.K.Stevenson
(2007).
Human follicular lymphoma cells contain oligomannose glycans in the antigen-binding site of the B-cell receptor.
|
| |
J Biol Chem,
282,
7405-7415.
|
|
|
|
|
|
|
E.W.Debler,
G.F.Kaufmann,
R.N.Kirchdoerfer,
J.M.Mee,
K.D.Janda,
and
I.A.Wilson
(2007).
Crystal structures of a quorum-quenching antibody.
|
| |
J Mol Biol,
368,
1392-1402.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.L.Pellequer,
S.W.Chen,
Y.S.Keum,
A.E.Karu,
Q.X.Li,
and
V.A.Roberts
(2005).
Structural basis for preferential binding of non-ortho-substituted polychlorinated biphenyls by the monoclonal antibody S2B1.
|
| |
J Mol Recognit,
18,
282-294.
|
|
|
|
|
|
|
S.Cho,
C.P.Swaminathan,
J.Yang,
M.C.Kerzic,
R.Guan,
M.C.Kieke,
D.M.Kranz,
R.A.Mariuzza,
and
E.J.Sundberg
(2005).
Structural basis of affinity maturation and intramolecular cooperativity in a protein-protein interaction.
|
| |
Structure,
13,
1775-1787.
|
|
|
|
|
|
|
J.B.Delehanty,
R.M.Jones,
T.C.Bishop,
and
D.A.Blake
(2003).
Identification of important residues in metal-chelate recognition by monoclonal antibodies.
|
| |
Biochemistry,
42,
14173-14183.
|
|
|
|
|
|
|
Y.Li,
H.Li,
F.Yang,
S.J.Smith-Gill,
and
R.A.Mariuzza
(2003).
X-ray snapshots of the maturation of an antibody response to a protein antigen.
|
| |
Nat Struct Biol,
10,
482-488.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
K.Murase,
R.Mizutani,
and
Y.Satow
(2001).
Expression, characterization and crystallization of the Fv fragment of mouse antibody 3B62 from the secondary immune response.
|
| |
Acta Crystallogr D Biol Crystallogr,
57,
1703-1705.
|
|
|
|
|
|
|
L.M.Wright,
A.M.Brzozowski,
R.E.Hubbard,
A.C.Pike,
S.M.Roberts,
R.N.Skovgaard,
I.Svendsen,
H.Vissing,
and
R.P.Bywater
(2000).
Structure of Fab hGR-2 F6, a competitive antagonist of the glucagon receptor.
|
| |
Acta Crystallogr D Biol Crystallogr,
56,
573-580.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.L.Pellequer,
S.Chen,
V.A.Roberts,
J.A.Tainer,
and
E.D.Getzoff
(1999).
Unraveling the effect of changes in conformation and compactness at the antibody V(L)-V(H) interface upon antigen binding.
|
| |
J Mol Recognit,
12,
267-275.
|
|
|
|
|
|
|
K.Furukawa,
A.Akasako-Furukawa,
H.Shirai,
H.Nakamura,
and
T.Azuma
(1999).
Junctional amino acids determine the maturation pathway of an antibody.
|
| |
Immunity,
11,
329-338.
|
|
|
|
|
|
|
M.Nakasako,
T.Motoyama,
Y.Kurahashi,
and
I.Yamaguchi
(1998).
Cryogenic X-ray crystal structure analysis for the complex of scytalone dehydratase of a rice blast fungus and its tight-binding inhibitor, carpropamid: the structural basis of tight-binding inhibition.
|
| |
Biochemistry,
37,
9931-9939.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
T.Azuma
(1998).
Somatic hypermutation in mouse lambda chains.
|
| |
Immunol Rev,
162,
97.
|
|
|
|
|
|
|
L.O.Hansson,
M.Widersten,
and
B.Mannervik
(1997).
Mechanism-based phage display selection of active-site mutants of human glutathione transferase A1-1 catalyzing SNAr reactions.
|
| |
Biochemistry,
36,
11252-11260.
|
|
|
|
|
|
|
X.Y.Pei,
P.Holliger,
A.G.Murzin,
and
R.L.Williams
(1997).
The 2.0-A resolution crystal structure of a trimeric antibody fragment with noncognate VH-VL domain pairs shows a rearrangement of VH CDR3.
|
| |
Proc Natl Acad Sci U S A,
94,
9637-9642.
|
|
|
PDB code:
|
|
|
|
|
|
|
The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
|
 |
Links
