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Contents |
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121 a.a.
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108 a.a.
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85 a.a.
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92 a.a.
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* Residue conservation analysis
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PDB id:
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Immune system
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Title:
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Antibody multispecificity mediated by conformational diversity
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Structure:
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Immunoglobulin e. Chain: h, j. Fragment: fv region, residues 1-122. Engineered: yes. Immunoglobulin e. Chain: l, m, n, o. Fragment: fv region, residues 1-110. Engineered: yes
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Source:
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Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: expressed as recombinant fv in e.Coli. Other_details: expressed as recombinant fv in e.Coli
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Biol. unit:
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Dimer (from PDB file)
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Resolution:
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2.66Å
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R-factor:
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0.226
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R-free:
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0.280
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Authors:
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L.C.James,P.Roversi,D.Tawfik
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Key ref:
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L.C.James
et al.
(2003).
Antibody multispecificity mediated by conformational diversity.
Science,
299,
1362-1367.
PubMed id:
DOI:
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Date:
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21-Jan-03
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Release date:
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15-Jan-04
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PROCHECK
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Headers
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References
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No UniProt id for this chain
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P01724
(LV1B_MOUSE) -
Ig lambda-1 chain V regions MOPC 104E/RPC20/J558/S104 from Mus musculus
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Seq:
Struc:
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129 a.a.
108 a.a.*
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DOI no:
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Science
299:1362-1367
(2003)
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PubMed id:
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Antibody multispecificity mediated by conformational diversity.
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L.C.James,
P.Roversi,
D.S.Tawfik.
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ABSTRACT
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A single antibody was shown to adopt different binding-site conformations and
thereby bind unrelated antigens. Analysis by both x-ray crystallography and
pre-steady-state kinetics revealed an equilibrium between different preexisting
isomers, one of which possessed a promiscuous, low-affinity binding site for
aromatic ligands, including the immunizing hapten. A subsequent induced-fit
isomerization led to high-affinity complexes with a deep and narrow binding
site. A protein antigen identified by repertoire selection made use of an
unrelated antibody isomer with a wide, shallow binding site. Conformational
diversity, whereby one sequence adopts multiple structures and multiple
functions, can increase the effective size of the antibody repertoire but may
also lead to autoimmunity and allergy.
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Selected figure(s)
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Figure 1.
Fig. 1. The four different isomers of IgE antibody SPE7. A
close-up view of the binding site is shown as a semitransparent
surface, colored according to electrostatic potential (blue for
positive, red for negative). The figure was prepared with GRASP
(39, 40) and AESOP (41). The Ab^3 and Ab^4 models are presented
without ligand.
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Figure 2.
Fig. 2. Details of SPE7's binding site and main-chain
superposition of isomers. (A to C) Hapten-bound SPE7 with (A)
DNP-Ser, (B) Az, and (C) Fur. Putative hydrogen bonds are
indicated by dotted spheres between acceptor and donor atoms.
(D) Main-chain configurations of free isomers Ab^1 (green) and
Ab^2 (purple), hapten-bound isomer Ab^3 (blue), and
Trx-Shear3-bound isomer Ab^4 (ochre). All figures were prepared
with SETOR (41).
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The above figures are
reprinted
by permission from the AAAs:
Science
(2003,
299,
1362-1367)
copyright 2003.
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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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R.P.Joosten,
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Acta Crystallogr D Biol Crystallogr,
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Neutralizing human monoclonal antibodies binding multiple serotypes of botulinum neurotoxin.
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Protein Eng Des Sel,
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J.D.Durrant,
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(2011).
Biochemical and structural characterization of lysophosphatidic Acid binding by a humanized monoclonal antibody.
|
| |
J Mol Biol,
408,
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PDB codes:
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J.S.Fraser,
and
C.J.Jackson
(2011).
Mining electron density for functionally relevant protein polysterism in crystal structures.
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| |
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S.J.Norwood,
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and
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Assembly and solution structure of the core retromer protein complex.
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PDB codes:
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S.R.Tzeng,
and
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PDB codes:
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E.J.Helmreich
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Ways and means of coping with uncertainties of the relationship of the genetic blue print to protein structure and function in the cell.
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Mapping the interactions between a major pollen allergen and human IgE antibodies.
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| |
Structure,
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PDB code:
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|
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H.N.Eisen,
and
A.K.Chakraborty
(2010).
Evolving concepts of specificity in immune reactions.
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Proc Natl Acad Sci U S A,
107,
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L.M.Iyer,
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Z.Pancer,
and
R.A.Mariuzza
(2010).
A structural basis for antigen recognition by the T cell-like lymphocytes of sea lamprey.
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Proc Natl Acad Sci U S A,
107,
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PDB codes:
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L.M.Ylinen,
A.J.Price,
J.Rasaiyaah,
S.Hué,
N.J.Rose,
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and
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(2010).
Conformational adaptation of Asian macaque TRIMCyp directs lineage specific antiviral activity.
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PDB codes:
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M.Cardó-Vila,
R.J.Giordano,
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(2010).
Structural and thermodynamic analysis of the GFP:GFP-nanobody complex.
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Protein Sci,
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PDB code:
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M.Lignell,
and
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(2010).
Recognition and binding of a helix-loop-helix peptide to carbonic anhydrase occurs via partly folded intermediate structures.
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Biophys J,
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and
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and
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(2010).
Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain.
|
| |
J Mol Biol,
396,
1128-1144.
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PDB code:
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R.A.Mariuzza,
C.A.Velikovsky,
L.Deng,
G.Xu,
and
Z.Pancer
(2010).
Structural insights into the evolution of the adaptive immune system: the variable lymphocyte receptors of jawless vertebrates.
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F.Ricci,
and
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Thermodynamic basis for the optimization of binding-induced biomolecular switches and structure-switching biosensors.
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M.C.Kerzic,
L.Aravind,
Z.Pancer,
and
R.A.Mariuzza
(2009).
Structure of a lamprey variable lymphocyte receptor in complex with a protein antigen.
|
| |
Nat Struct Mol Biol,
16,
725-730.
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PDB codes:
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C.J.López,
M.R.Fleissner,
Z.Guo,
A.K.Kusnetzow,
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The role of dynamic conformational ensembles in biomolecular recognition.
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Induced fit for mRNA/TIS11d complex.
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J Chem Phys,
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Modeling signal propagation mechanisms and ligand-based conformational dynamics of the Hsp90 molecular chaperone full-length dimer.
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H.F.Chen
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Molecular dynamics simulation of phosphorylated KID post-translational modification.
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Immunotherapy,
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Variants of the antibody herceptin that interact with HER2 and VEGF at the antigen binding site.
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PDB codes:
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PDB codes:
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PDB codes:
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PDB codes:
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(2008).
Anchored plasticity opens doors for selective inhibitor design in nitric oxide synthase.
|
| |
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PDB codes:
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|
|
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|
|
E.W.Debler,
R.Müller,
D.Hilvert,
and
I.A.Wilson
(2008).
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| |
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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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