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214 a.a.
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223 a.a.
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105 a.a.
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* Residue conservation analysis
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PDB id:
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Complex (antibody/electron transport)
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Title:
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Igg1 fab fragment (of e8 antibody) complexed with horse cytochromE C at 1.8 a resolution
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Structure:
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E8 antibody. Chain: l. Fragment: fab. Synonym: fab e8. Other_details: igg1 kappa mouse monoclonal antibody. E8 antibody. Chain: h. Fragment: fab. Synonym: fab e8.
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Source:
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Mus musculus. House mouse. Organism_taxid: 10090. Strain: balb/c. Cell_line: p3-x63-ag8.653. Organ: spleen. Other_details: e8 antibody purified from ascites. Strain: balb-c. Equus caballus.
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Biol. unit:
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Monomer (from PDB file)
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Resolution:
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1.80Å
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R-factor:
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0.200
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R-free:
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0.256
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Authors:
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S.E.Mylvaganam,Y.Paterson,E.D.Getzoff
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Key ref:
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S.E.Mylvaganam
et al.
(1998).
Structural basis for the binding of an anti-cytochrome c antibody to its antigen: crystal structures of FabE8-cytochrome c complex to 1.8 A resolution and FabE8 to 2.26 A resolution.
J Mol Biol,
281,
301-322.
PubMed id:
DOI:
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Date:
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26-Mar-98
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Release date:
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09-Dec-98
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PROCHECK
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Headers
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References
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P01635
(KV5A3_MOUSE) -
Immunoglobulin kappa chain variable 12-41 (Fragment) from Mus musculus
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Seq:
Struc:
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115 a.a.
214 a.a.
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DOI no:
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J Mol Biol
281:301-322
(1998)
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PubMed id:
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Structural basis for the binding of an anti-cytochrome c antibody to its antigen: crystal structures of FabE8-cytochrome c complex to 1.8 A resolution and FabE8 to 2.26 A resolution.
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S.E.Mylvaganam,
Y.Paterson,
E.D.Getzoff.
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ABSTRACT
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A complete understanding of antibody-antigen association and specificity
requires the stereochemical description of both antigen and antibody before and
upon complex formation. The structural mechanism involved in the binding of the
IgG1 monoclonal antibody E8 to its highly charged protein antigen horse
cytochrome c (cyt c) is revealed by crystallographic structures of the
antigen-binding fragment (Fab) of E8 bound to cyt c (FabE8-cytc), determined to
1.8 A resolution, and of uncomplexed Fab E8 (FabE8), determined to 2.26 A
resolution. E8 antibody binds to three major discontiguous segments (33 to 39;
56 to 66; 96 to 104), and two minor sites on cyt c opposite to the exposed haem
edge. Crystallographic definition of the E8 epitope complements and extends
biochemical mapping and two-dimensional nuclear magnetic resonance with
hydrogen-deuterium exchange studies. These combined results demonstrate that
antibody-induced stabilization of secondary structural elements within the
antigen can propagate locally to adjacent residues outside the epitope.
Pre-existing shape complementarity at the FabE8-cytc interface is enhanced by 48
bound water molecules, and by local movements of up to 4.2 A for E8 antibody and
8.9 A for cyt c. Glu62, Asn103 and the C-terminal Glu104 of cyt c adjust to fit
the pre-formed VL "hill" and VH "valley" shape of the
grooved E8 paratope. All six E8 complementarity determining regions (CDRs)
contact the antigen, with CDR L1 forming 46% of the total atomic contacts, and
CDRs L1 (29%) and H3 (20%) contributing the highest percentage of the total
surface area of E8 buried by cyt c (550 A2). The E8 antibody covers 534 A2 of
the cyt c surface. The formation of five ion pairs between E8 and flexible cyt c
residues Lys60, Glu62 and Glu104 suggests the importance of mobile regions and
electrostatic interactions in providing the exquisite specificity needed for
recognition of this extremely conserved protein antigen. The highly homologous
VL domains of E8 and anti-lysozyme antibody D1. 3 achieve their distinct
antigen-binding specificities by expanding the impact of their limited sequence
differences through the recruitment of different sets of conserved residues and
distinctly different CDR L3 conformations.
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Selected figure(s)
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Figure 1.
Figure 1. Stereo views of FabE8-cyt c complex and FabE8
X-ray structures. a, Ribbon representation of the FabE8-cyt c
interface region. E8 V-domain (V[L], white; V[H], yellow) and
cyt c (orange). Highlighted are the three major discontiguous
segments of E8 epitope on cyt c (33 to 39, 56 to 66 and 96 to
104 in red) and the six E8 CDRs (L1 and H1, red; L2 and H2,
yellow; L3 and H3, green). b, Ribbon representation of the FabE8
(pink) and FabE8-cyt c (L, white; H, yellow; cyt c, orange)
structures with V-domains superimposed. The elbow angles of the
two structures differ by 6°. c, Cyt c (orange) bound to
CDR-H3 of FabE8-cyt c (yellow), with CDR-H3 of D1.3Fv-HEL
(purple) superimposed. The tip of E8 H3 (top) complements the
second 30 s type II b-turn (35 to 38) of cyt c. E8 Phe91L and
Trp96L of L3 (white) and Tyr33H1 (yellow) neighbour E8 H3. The
base of E8 H3 is in the extended conformation and the
carboxylate group of Asp105H3[101] hydrogen bonds with the
Trp107H[103] FR4 and Tyr36L FR2 side-chains. In the D1.3
antibody (purple), the base of H3 is "kinked" at position [101].
The Asp side-chain at this position is flipped 180° with
respect to E8 Asp105H3[101] and ion pairs with ArgH3[94]
(equivalent position Gly98H in E8). Oxygen and nitrogen atoms
are shown as red and blue spheres, respectively and hydrogen
bonds as yellow dotted lines.
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Figure 3.
Figure 3. Stereo views of buried surface areas and residues
of the FabE8-cyt c (a) paratope with 48 interface water
molecules, and (b) E8 epitope. Views are 90° fromFigure 1a.
Water molecules (green spheres) form a collar around the buried
surface areas of E8 antibody (pink mesh) and cyt c (blue mesh).
C^a traces of E8 V[L] are shown in white, V[H] in yellow and cyt
c in orange. Side-chains in the E8 paratope are displayed and
labelled with CDRs L1 and H1 in red, L2 and H2 in yellow and L3
and H3 in green. The E8 epitope consists of three major
discontiguous segments (33 to 39; 56 to 66 and 96 to 104) shown
with magenta side-chains and two minor sites composed of the
N-terminal acetyl group (Ac), Val3 (top) and Lys22 (left) (with
white side-chains and yellow labels) at the periphery. Arg38 and
Tyr74 (white side-chains and green labels) lie outside the E8
epitope. Oxygen and nitrogen atoms are shown as red and blue
spheres, respectively.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1998,
281,
301-322)
copyright 1998.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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C.J.Tape,
S.H.Willems,
S.L.Dombernowsky,
P.L.Stanley,
M.Fogarasi,
W.Ouwehand,
J.McCafferty,
and
G.Murphy
(2011).
Cross-domain inhibition of TACE ectodomain.
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Proc Natl Acad Sci U S A,
108,
5578-5583.
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I.Bertini,
G.Cavallaro,
and
A.Rosato
(2011).
Principles and patterns in the interaction between mono-heme cytochrome c and its partners in electron transfer processes.
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Metallomics,
3,
354-362.
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A.Malik,
A.Firoz,
V.Jha,
E.Sunderasan,
and
S.Ahmad
(2010).
Modeling the three-dimensional structures of an unbound single-chain variable fragment (scFv) and its hypothetical complex with a Corynespora cassiicola toxin, cassiicolin.
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J Mol Model,
16,
1883-1893.
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K.R.Abhinandan,
and
A.C.Martin
(2010).
Analysis and prediction of VH/VL packing in antibodies.
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Protein Eng Des Sel,
23,
689-697.
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M.B.Irving,
L.Craig,
A.Menendez,
B.P.Gangadhar,
M.Montero,
N.E.van Houten,
and
J.K.Scott
(2010).
Exploring peptide mimics for the production of antibodies against discontinuous protein epitopes.
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Mol Immunol,
47,
1137-1148.
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C.E.Leysath,
A.F.Monzingo,
J.A.Maynard,
J.Barnett,
G.Georgiou,
B.L.Iverson,
and
J.D.Robertus
(2009).
Crystal structure of the engineered neutralizing antibody M18 complexed to domain 4 of the anthrax protective antigen.
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J Mol Biol,
387,
680-693.
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PDB codes:
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J.Bostrom,
S.F.Yu,
D.Kan,
B.A.Appleton,
C.V.Lee,
K.Billeci,
W.Man,
F.Peale,
S.Ross,
C.Wiesmann,
and
G.Fuh
(2009).
Variants of the antibody herceptin that interact with HER2 and VEGF at the antigen binding site.
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Science,
323,
1610-1614.
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PDB codes:
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S.J.Coales,
S.J.Tuske,
J.C.Tomasso,
and
Y.Hamuro
(2009).
Epitope mapping by amide hydrogen/deuterium exchange coupled with immobilization of antibody, on-line proteolysis, liquid chromatography and mass spectrometry.
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Rapid Commun Mass Spectrom,
23,
639-647.
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A.Sivasubramanian,
J.A.Maynard,
and
J.J.Gray
(2008).
Modeling the structure of mAb 14B7 bound to the anthrax protective antigen.
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Proteins,
70,
218-230.
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E.O.Saphire,
M.Montero,
A.Menendez,
N.E.van Houten,
M.B.Irving,
R.Pantophlet,
M.B.Zwick,
P.W.Parren,
D.R.Burton,
J.K.Scott,
and
I.A.Wilson
(2007).
Structure of a high-affinity "mimotope" peptide bound to HIV-1-neutralizing antibody b12 explains its inability to elicit gp120 cross-reactive antibodies.
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J Mol Biol,
369,
696-709.
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R.J.Duquesnoy
(2006).
A structurally based approach to determine HLA compatibility at the humoral immune level.
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Hum Immunol,
67,
847-862.
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B.Peters,
J.Sidney,
P.Bourne,
H.H.Bui,
S.Buus,
G.Doh,
W.Fleri,
M.Kronenberg,
R.Kubo,
O.Lund,
D.Nemazee,
J.V.Ponomarenko,
M.Sathiamurthy,
S.P.Schoenberger,
S.Stewart,
P.Surko,
S.Way,
S.Wilson,
and
A.Sette
(2005).
The design and implementation of the immune epitope database and analysis resource.
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Immunogenetics,
57,
326-336.
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D.Segal,
and
M.Eisenstein
(2005).
The effect of resolution-dependent global shape modifications on rigid-body protein-protein docking.
|
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Proteins,
59,
580-591.
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G.H.Cohen,
E.W.Silverton,
E.A.Padlan,
F.Dyda,
J.A.Wibbenmeyer,
R.C.Willson,
and
D.R.Davies
(2005).
Water molecules in the antibody-antigen interface of the structure of the Fab HyHEL-5-lysozyme complex at 1.7 A resolution: comparison with results from isothermal titration calorimetry.
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Acta Crystallogr D Biol Crystallogr,
61,
628-633.
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PDB code:
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A.Berchanski,
B.Shapira,
and
M.Eisenstein
(2004).
Hydrophobic complementarity in protein-protein docking.
|
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Proteins,
56,
130-142.
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M.Geva,
M.Eisenstein,
and
L.Addadi
(2004).
Antibody recognition of chiral surfaces. Structural models of antibody complexes with leucine-leucine-tyrosine crystal surfaces.
|
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Proteins,
55,
862-873.
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W.D.Crill,
and
G.J.Chang
(2004).
Localization and characterization of flavivirus envelope glycoprotein cross-reactive epitopes.
|
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J Virol,
78,
13975-13986.
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L.O.Essen,
A.Harrenga,
C.Ostermeier,
and
H.Michel
(2003).
1.3 A X-ray structure of an antibody Fv fragment used for induced membrane-protein crystallization.
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Acta Crystallogr D Biol Crystallogr,
59,
677-687.
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PDB code:
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J.G.Luz,
M.Huang,
K.C.Garcia,
M.G.Rudolph,
V.Apostolopoulos,
L.Teyton,
and
I.A.Wilson
(2002).
Structural comparison of allogeneic and syngeneic T cell receptor-peptide-major histocompatibility complex complexes: a buried alloreactive mutation subtly alters peptide presentation substantially increasing V(beta) Interactions.
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J Exp Med,
195,
1175-1186.
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PDB codes:
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S.Michel,
E.Forest,
Y.Pétillot,
G.Deléage,
N.Heuzé-Vourc'h,
Y.Courty,
D.Lascoux,
M.Jolivet,
and
C.Jolivet-Reynaud
(2001).
Involvement of the C-terminal end of the prostrate-specific antigen in a conformational epitope: characterization by proteolytic degradation of monoclonal antibody-bound antigen and mass spectrometry.
|
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J Mol Recognit,
14,
406-413.
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S.Monaco-Malbet,
C.Berthet-Colominas,
A.Novelli,
N.Battaï,
N.Piga,
V.Cheynet,
F.Mallet,
and
S.Cusack
(2000).
Mutual conformational adaptations in antigen and antibody upon complex formation between an Fab and HIV-1 capsid protein p24.
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Structure,
8,
1069-1077.
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PDB codes:
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Y.Li,
H.Li,
S.J.Smith-Gill,
and
R.A.Mariuzza
(2000).
Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63(,).
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Biochemistry,
39,
6296-6309.
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PDB codes:
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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.
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J Mol Recognit,
12,
267-275.
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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.
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Links
