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Contents |
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* Residue conservation analysis
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PDB id:
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Immune system, lysozyme
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Title:
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Degenerate interfaces in antigen-antibody complexes
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Structure:
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Vh single-domain antibody. Chain: a. Fragment: vh domain fragment. Engineered: yes. Lysozyme. Chain: l. Fragment: enzyme. Synonym: 1,4-beta-n-acetylmuramidasE C, allergen gal d iv. Ec: 3.2.1.17
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Source:
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Camelus dromedarius. Arabian camel. Organism_taxid: 9838. Expressed in: escherichia coli. Expression_system_taxid: 562. Gallus gallus. Chicken. Organism_taxid: 9031. Other_details: purchased from sigma
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Biol. unit:
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Tetramer (from
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Resolution:
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2.10Å
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R-factor:
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0.164
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R-free:
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0.204
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Authors:
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K.Decanniere,T.R.Transue,A.Desmyter,D.Maes,S.Muyldermans,L.Wyns
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Key ref:
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K.Decanniere
et al.
(2001).
Degenerate interfaces in antigen-antibody complexes.
J Mol Biol,
313,
473-478.
PubMed id:
DOI:
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Date:
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22-Aug-01
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Release date:
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05-Dec-01
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PROCHECK
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Headers
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References
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Enzyme class:
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Chain L:
E.C.3.2.1.17
- lysozyme.
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Reaction:
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Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.
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DOI no:
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J Mol Biol
313:473-478
(2001)
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PubMed id:
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Degenerate interfaces in antigen-antibody complexes.
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K.Decanniere,
T.R.Transue,
A.Desmyter,
D.Maes,
S.Muyldermans,
L.Wyns.
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ABSTRACT
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In most of the work dealing with the analysis of protein-protein interfaces, a
single X-ray structure is available or selected, and implicitly it is assumed
that this structure corresponds to the optimal complex for this pair of
proteins. However, we have found a degenerate interface in a high-affinity
antibody-antigen complex: the two independent complexes of the camel variable
domain antibody fragment cAb-Lys3 and its antigen hen egg white lysozyme present
in the asymmetric unit of our crystals show a difference in relative orientation
between antibody and antigen, leading to important differences at the
protein-protein interface. A third cAb-Lys3-hen lysozyme complex in a different
crystal form adopts yet another relative orientation. Our results show that
protein-protein interface characteristics can vary significantly between
different specimens of the same high-affinity antibody-protein antigen complex.
Consideration should be given to this type of observation when trying to
establish general protein-protein interface characteristics.
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Selected figure(s)
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Figure 1.
Figure 1. Superposition of the hel1 and hel2 com-
plexes: (a) using all main-chain atoms; (b) using main-
chain atoms of cAb-Lys3 only; (c) superposition as in
(b), comparing the hel1 complex with the hel-C2 com-
plex; (d) superposition as in (b), comparing the tel1 and
tel2 complexes. cAb-Lys3 molecules are in grey and
dark green, lysozyme is in yellow and blue.
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Figure 2.
Figure 2. Differences in (a) buried surface area and (b)
Voronoi volume for the cAb-Lys3 interface atoms
between the hel1 and hel2 complex. Dark colours rep-
resent little or no change, light colours represent large
differences. CDR1 atoms are coloured blue, CDR2 atoms
are yellow, and the CDR3 atoms are red. Green halos
around CDR3 atoms indicate atoms making hydrogen
bonds with the antigen. Framework atoms are grey.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2001,
313,
473-478)
copyright 2001.
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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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D.Smolarek,
C.Hattab,
G.Hassanzadeh-Ghassabeh,
S.Cochet,
C.Gutiérrez,
A.G.de Brevern,
R.Udomsangpetch,
J.Picot,
M.Grodecka,
K.Wasniowska,
S.Muyldermans,
Y.Colin,
C.Le Van Kim,
M.Czerwinski,
and
O.Bertrand
(2010).
A recombinant dromedary antibody fragment (VHH or nanobody) directed against human Duffy antigen receptor for chemokines.
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Cell Mol Life Sci,
67,
3371-3387.
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M.H.Kubala,
O.Kovtun,
K.Alexandrov,
and
B.M.Collins
(2010).
Structural and thermodynamic analysis of the GFP:GFP-nanobody complex.
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Protein Sci,
19,
2389-2401.
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PDB code:
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A.Mascioni,
B.E.Bentley,
R.Camarda,
D.A.Dilts,
P.Fink,
V.Gusarova,
S.K.Hoiseth,
J.Jacob,
S.L.Lin,
K.Malakian,
L.K.McNeil,
T.Mininni,
F.Moy,
E.Murphy,
E.Novikova,
S.Sigethy,
Y.Wen,
G.W.Zlotnick,
and
D.H.Tsao
(2009).
Structural Basis for the Immunogenic Properties of the Meningococcal Vaccine Candidate LP2086.
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J Biol Chem,
284,
8738-8746.
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PDB code:
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C.Vincke,
R.Loris,
D.Saerens,
S.Martinez-Rodriguez,
S.Muyldermans,
and
K.Conrath
(2009).
General Strategy to Humanize a Camelid Single-domain Antibody and Identification of a Universal Humanized Nanobody Scaffold.
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J Biol Chem,
284,
3273-3284.
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PDB codes:
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K.Conrath,
A.S.Pereira,
C.E.Martins,
C.G.Timóteo,
P.Tavares,
S.Spinelli,
J.Kinne,
C.Flaudrops,
C.Cambillau,
S.Muyldermans,
I.Moura,
J.J.Moura,
M.Tegoni,
and
A.Desmyter
(2009).
Camelid nanobodies raised against an integral membrane enzyme, nitric oxide reductase.
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Protein Sci,
18,
619-628.
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O.Martin,
and
D.Schomburg
(2008).
Efficient comprehensive scoring of docked protein complexes using probabilistic support vector machines.
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Proteins,
70,
1367-1378.
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V.Lafont,
M.Schaefer,
R.H.Stote,
D.Altschuh,
and
A.Dejaegere
(2007).
Protein-protein recognition and interaction hot spots in an antigen-antibody complex: free energy decomposition identifies "efficient amino acids".
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Proteins,
67,
418-434.
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Y.Wu,
C.Eigenbrot,
W.C.Liang,
S.Stawicki,
S.Shia,
B.Fan,
R.Ganesan,
M.T.Lipari,
and
D.Kirchhofer
(2007).
Structural insight into distinct mechanisms of protease inhibition by antibodies.
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Proc Natl Acad Sci U S A,
104,
19784-19789.
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PDB codes:
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A.Marquardt,
S.Muyldermans,
and
M.Przybylski
(2006).
A synthetic camel anti-lysozyme peptide antibody (peptibody) with flexible loop structure identified by high-resolution affinity mass spectrometry.
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Chemistry,
12,
1915-1923.
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E.De Genst,
K.Silence,
K.Decanniere,
K.Conrath,
R.Loris,
J.Kinne,
S.Muyldermans,
and
L.Wyns
(2006).
Molecular basis for the preferential cleft recognition by dromedary heavy-chain antibodies.
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Proc Natl Acad Sci U S A,
103,
4586-4591.
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PDB codes:
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F.Cantini,
S.Savino,
M.Scarselli,
V.Masignani,
M.Pizza,
G.Romagnoli,
E.Swennen,
D.Veggi,
L.Banci,
and
R.Rappuoli
(2006).
Solution structure of the immunodominant domain of protective antigen GNA1870 of Neisseria meningitidis.
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J Biol Chem,
281,
7220-7227.
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PDB code:
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R.H.Lilien,
B.W.Stevens,
A.C.Anderson,
and
B.R.Donald
(2005).
A novel ensemble-based scoring and search algorithm for protein redesign and its application to modify the substrate specificity of the gramicidin synthetase a phenylalanine adenylation enzyme.
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J Comput Biol,
12,
740-761.
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E.De Genst,
F.Handelberg,
A.Van Meirhaeghe,
S.Vynck,
R.Loris,
L.Wyns,
and
S.Muyldermans
(2004).
Chemical basis for the affinity maturation of a camel single domain antibody.
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J Biol Chem,
279,
53593-53601.
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PDB code:
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R.L.Stanfield,
H.Dooley,
M.F.Flajnik,
and
I.A.Wilson
(2004).
Crystal structure of a shark single-domain antibody V region in complex with lysozyme.
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Science,
305,
1770-1773.
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PDB codes:
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C.H.Li,
X.H.Ma,
W.Z.Chen,
and
C.X.Wang
(2003).
A soft docking algorithm for predicting the structure of antibody-antigen complexes.
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Proteins,
52,
47-50.
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E.Ben-Zeev,
A.Berchanski,
A.Heifetz,
B.Shapira,
and
M.Eisenstein
(2003).
Prediction of the unknown: inspiring experience with the CAPRI experiment.
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Proteins,
52,
41-46.
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E.De Genst,
D.Areskoug,
K.Decanniere,
S.Muyldermans,
and
K.Andersson
(2002).
Kinetic and affinity predictions of a protein-protein interaction using multivariate experimental design.
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J Biol Chem,
277,
29897-29907.
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G.R.Smith,
and
M.J.Sternberg
(2002).
Prediction of protein-protein interactions by docking methods.
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Curr Opin Struct Biol,
12,
28-35.
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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
code is
shown on the right.
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Links
