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PDBsum entry 1l3w
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Cell adhesion, metal binding protein
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PDB id
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1l3w
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Contents |
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* Residue conservation analysis
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DOI no:
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Science
296:1308-1313
(2002)
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PubMed id:
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C-cadherin ectodomain structure and implications for cell adhesion mechanisms.
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T.J.Boggon,
J.Murray,
S.Chappuis-Flament,
E.Wong,
B.M.Gumbiner,
L.Shapiro.
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ABSTRACT
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Cadherins are transmembrane proteins that mediate adhesion between cells in the
solid tissues of animals. Here we present the 3.1 angstrom resolution crystal
structure of the whole, functional extracellular domain from C-cadherin, a
representative "classical" cadherin. The structure suggests a
molecular mechanism for adhesion between cells by classical cadherins, and it
provides a new framework for understanding both cis (same cell) and trans
(juxtaposed cell) cadherin interactions. The trans adhesive interface is a
twofold symmetric interaction defined by a conserved tryptophan side chain at
the membrane-distal end of a cadherin molecule from one cell, which inserts into
a hydrophobic pocket at the membrane-distal end of a cadherin molecule from the
opposing cell.
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Selected figure(s)
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Figure 1.
Fig. 1. (A) Stereo view of the C-cadherin ectodomain. Trp2 is
shown in CPK representation and colored purple; green spheres,
calcium ions; cyan, disulfide bonds; red, O-linked sugars; blue,
N-linked sugars. Individual cadherin-like domains are labeled
EC1 through EC5. (B) View 90° away from (A). (C) An example
region of the 3f[obs] - 2f[calc] electron density map contoured
at 2  centered
on the strand dimer interface. (D) An example of the 2 3f[obs] -
2f[calc] density seen for glycosylation sites. Images made with
the program SETOR (35).
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Figure 3.
Fig. 3. Potential cis dimerization interface. (A) Comparison of
similar interfaces seen in the crystal structures of the
C-cadherin ectodomain (this work), and two structures of a
two-domain fragment from E-cadherin in space groups P2[1] (PDB
code 1FF5) and C2 (PDB code 1EDH). EC1 and EC2 domains are
shown. Primary regions of contact include the front  sheet of
EC1 (strands C, D, and F), which interact with residues mainly
from the back sheet of EC2 (strands B, D, and E). (B) Detailed
stereo view of the cis-oriented interface. Residues that make
direct contact in the interface are labeled, and calcium ions
are shown as green spheres. Primes indicate the partner
molecule. The conserved residue Asp44 in the quasi- -helix
region is in close proximity to the EC2 to EC3 calcium-binding
region, although direct ligation of calcium ions is not
observed. Images were made with the program SETOR (35).
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The above figures are
reprinted
by permission from the AAAs:
Science
(2002,
296,
1308-1313)
copyright 2002.
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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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E.Baranova,
R.Fronzes,
A.Garcia-Pino,
N.Van Gerven,
D.Papapostolou,
G.Péhau-Arnaudet,
E.Pardon,
J.Steyaert,
S.Howorka,
and
H.Remaut
(2012).
SbsB structure and lattice reconstruction unveil Ca2+ triggered S-layer assembly.
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Nature,
487,
119-122.
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PDB code:
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A.L.Smith,
D.B.Friedman,
H.Yu,
R.H.Carnahan,
and
A.B.Reynolds
(2011).
ReCLIP (Reversible Cross-Link Immuno-Precipitation): An Efficient Method for Interrogation of Labile Protein Complexes.
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PLoS One,
6,
e16206.
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C.P.Cifarelli,
B.Titus,
and
H.K.Yeoh
(2011).
Cadherin-dependent adhesion of human U373MG glioblastoma cells promotes neurite outgrowth and increases migratory capacity. Laboratory investigation.
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J Neurosurg,
114,
663-669.
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G.S.Brigidi,
and
S.X.Bamji
(2011).
Cadherin-catenin adhesion complexes at the synapse.
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Curr Opin Neurobiol,
21,
208-214.
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J.Brasch,
O.J.Harrison,
G.Ahlsen,
S.M.Carnally,
R.M.Henderson,
B.Honig,
and
L.Shapiro
(2011).
Structure and binding mechanism of vascular endothelial cadherin: a divergent classical cadherin.
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J Mol Biol,
408,
57-73.
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PDB code:
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J.Vendome,
S.Posy,
X.Jin,
F.Bahna,
G.Ahlsen,
L.Shapiro,
and
B.Honig
(2011).
Molecular design principles underlying β-strand swapping in the adhesive dimerization of cadherins.
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Nat Struct Mol Biol,
18,
693-700.
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PDB code:
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S.Hong,
R.B.Troyanovsky,
and
S.M.Troyanovsky
(2011).
Cadherin exits the junction by switching its adhesive bond.
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J Cell Biol,
192,
1073-1083.
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Y.Wu,
J.Vendome,
L.Shapiro,
A.Ben-Shaul,
and
B.Honig
(2011).
Transforming binding affinities from three dimensions to two with application to cadherin clustering.
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Nature,
475,
510-513.
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A.Pertsinidis,
Y.Zhang,
and
S.Chu
(2010).
Subnanometre single-molecule localization, registration and distance measurements.
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Nature,
466,
647-651.
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C.Ciatto,
F.Bahna,
N.Zampieri,
H.C.VanSteenhouse,
P.S.Katsamba,
G.Ahlsen,
O.J.Harrison,
J.Brasch,
X.Jin,
S.Posy,
J.Vendome,
B.Ranscht,
T.M.Jessell,
B.Honig,
and
L.Shapiro
(2010).
T-cadherin structures reveal a novel adhesive binding mechanism.
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Nat Struct Mol Biol,
17,
339-347.
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PDB codes:
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D.Garrod
(2010).
Desmosomes in vivo.
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Dermatol Res Pract,
2010,
212439.
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G.R.Owen,
and
D.L.Stokes
(2010).
Exploring the Nature of Desmosomal Cadherin Associations in 3D.
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Dermatol Res Pract,
2010,
930401.
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H.A.Thomason,
A.Scothern,
S.McHarg,
and
D.R.Garrod
(2010).
Desmosomes: adhesive strength and signalling in health and disease.
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Biochem J,
429,
419-433.
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H.M.Elledge,
P.Kazmierczak,
P.Clark,
J.S.Joseph,
A.Kolatkar,
P.Kuhn,
and
U.Müller
(2010).
Structure of the N terminus of cadherin 23 reveals a new adhesion mechanism for a subset of cadherin superfamily members.
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Proc Natl Acad Sci U S A,
107,
10708-10712.
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PDB code:
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J.Binkley,
K.Karra,
A.Kirby,
M.Hosobuchi,
E.A.Stone,
and
A.Sidow
(2010).
ProPhylER: a curated online resource for protein function and structure based on evolutionary constraint analyses.
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Genome Res,
20,
142-154.
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J.Yamagami,
A.S.Payne,
S.Kacir,
K.Ishii,
D.L.Siegel,
and
J.R.Stanley
(2010).
Homologous regions of autoantibody heavy chain complementarity-determining region 3 (H-CDR3) in patients with pemphigus cause pathogenicity.
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J Clin Invest,
120,
4111-4117.
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K.J.Green,
S.Getsios,
S.Troyanovsky,
and
L.M.Godsel
(2010).
Intercellular junction assembly, dynamics, and homeostasis.
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Cold Spring Harb Perspect Biol,
2,
a000125.
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M.Amagai
(2010).
Autoimmune and infectious skin diseases that target desmogleins.
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Proc Jpn Acad Ser B Phys Biol Sci,
86,
524-537.
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M.F.Izaguirre,
D.Larrea,
J.F.Adur,
J.E.Diaz-Zamboni,
N.B.Vicente,
C.D.Galetto,
and
V.H.Casco
(2010).
Role of E-cadherin in epithelial architecture maintenance.
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Cell Commun Adhes,
17,
1.
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M.F.Izaguirre,
and
V.H.Casco
(2010).
T3 regulates E-cadherin, and β- and α-catenin expression in the stomach during the metamorphosis of the toad Rhinella arenarum.
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Biotech Histochem,
85,
305-323.
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M.Sotomayor,
W.A.Weihofen,
R.Gaudet,
and
D.P.Corey
(2010).
Structural determinants of cadherin-23 function in hearing and deafness.
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Neuron,
66,
85.
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PDB codes:
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N.Ishiyama,
S.H.Lee,
S.Liu,
G.Y.Li,
M.J.Smith,
L.F.Reichardt,
and
M.Ikura
(2010).
Dynamic and static interactions between p120 catenin and E-cadherin regulate the stability of cell-cell adhesion.
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Cell,
141,
117-128.
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PDB codes:
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O.J.Harrison,
F.Bahna,
P.S.Katsamba,
X.Jin,
J.Brasch,
J.Vendome,
G.Ahlsen,
K.J.Carroll,
S.R.Price,
B.Honig,
and
L.Shapiro
(2010).
Two-step adhesive binding by classical cadherins.
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Nat Struct Mol Biol,
17,
348-357.
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PDB codes:
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S.I.O'Donoghue,
D.S.Goodsell,
A.S.Frangakis,
F.Jossinet,
R.A.Laskowski,
M.Nilges,
H.R.Saibil,
A.Schafferhans,
R.C.Wade,
E.Westhof,
and
A.J.Olson
(2010).
Visualization of macromolecular structures.
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Nat Methods,
7,
S42-S55.
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S.K.Chang,
Z.Gu,
and
M.B.Brenner
(2010).
Fibroblast-like synoviocytes in inflammatory arthritis pathology: the emerging role of cadherin-11.
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Immunol Rev,
233,
256-266.
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S.Kamran-ul-Hassan Naqvi,
Z.Azeem,
G.Ali,
and
W.Ahmad
(2010).
A novel splice-acceptor site mutation in CDH3 gene in a consanguineous family exhibiting hypotrichosis with juvenile macular dystrophy.
|
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Arch Dermatol Res,
302,
701-703.
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S.Kjaer,
S.Hanrahan,
N.Totty,
and
N.Q.McDonald
(2010).
Mammal-restricted elements predispose human RET to folding impairment by HSCR mutations.
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Nat Struct Mol Biol,
17,
726-731.
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PDB code:
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Y.Sugawara,
T.Matsumura,
Y.Takegahara,
Y.Jin,
Y.Tsukasaki,
M.Takeichi,
and
Y.Fujinaga
(2010).
Botulinum hemagglutinin disrupts the intercellular epithelial barrier by directly binding E-cadherin.
|
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J Cell Biol,
189,
691-700.
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Y.Wu,
X.Jin,
O.Harrison,
L.Shapiro,
B.H.Honig,
and
A.Ben-Shaul
(2010).
Cooperativity between trans and cis interactions in cadherin-mediated junction formation.
|
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Proc Natl Acad Sci U S A,
107,
17592-17597.
|
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D.Osumi,
M.Takahashi,
E.Miyoshi,
S.Yokoe,
S.H.Lee,
K.Noda,
S.Nakamori,
J.Gu,
Y.Ikeda,
Y.Kuroki,
K.Sengoku,
M.Ishikawa,
and
N.Taniguchi
(2009).
Core fucosylation of E-cadherin enhances cell-cell adhesion in human colon carcinoma WiDr cells.
|
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Cancer Sci,
100,
888-895.
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E.Carico,
F.Fulciniti,
M.R.Giovagnoli,
N.S.Losito,
G.Botti,
G.Benincasa,
M.G.Farnetano,
and
A.Vecchione
(2009).
Adhesion molecules and p16 expression in endocervical adenocarcinoma.
|
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Virchows Arch,
455,
245-251.
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E.H.Lee,
J.Hsin,
M.Sotomayor,
G.Comellas,
and
K.Schulten
(2009).
Discovery through the computational microscope.
|
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Structure,
17,
1295-1306.
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E.Klaile,
O.Vorontsova,
K.Sigmundsson,
M.M.Müller,
B.B.Singer,
L.G.Ofverstedt,
S.Svensson,
U.Skoglund,
and
B.Obrink
(2009).
The CEACAM1 N-terminal Ig domain mediates cis- and trans-binding and is essential for allosteric rearrangements of CEACAM1 microclusters.
|
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J Cell Biol,
187,
553-567.
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H.B.Guo,
H.Johnson,
M.Randolph,
and
M.Pierce
(2009).
Regulation of homotypic cell-cell adhesion by branched N-glycosylation of N-cadherin extracellular EC2 and EC3 domains.
|
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J Biol Chem,
284,
34986-34997.
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J.Liang,
and
J.M.Fernández
(2009).
Mechanochemistry: One Bond at a Time.
|
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ACS Nano,
3,
1628-1645.
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K.Zheng,
J.S.Laurence,
K.Kuczera,
G.Verkhivker,
C.R.Middaugh,
and
T.J.Siahaan
(2009).
Characterization of multiple stable conformers of the EC5 domain of E-cadherin and the interaction of EC5 with E-cadherin peptides.
|
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Chem Biol Drug Des,
73,
584-598.
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L.Raptis,
R.Arulanandam,
A.Vultur,
M.Geletu,
S.Chevalier,
and
H.Feracci
(2009).
Beyond structure, to survival: activation of Stat3 by cadherin engagement.
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Biochem Cell Biol,
87,
835-843.
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L.Shapiro,
and
W.I.Weis
(2009).
Structure and biochemistry of cadherins and catenins.
|
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Cold Spring Harbor Perspect Biol,
1,
a003053.
|
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M.Jelani,
M.Salman Chishti,
and
W.Ahmad
(2009).
A novel splice-site mutation in the CDH3 gene in hypotrichosis with juvenile macular dystrophy.
|
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Clin Exp Dermatol,
34,
68-73.
|
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M.Trivedi,
R.A.Davis,
Y.Shabaik,
A.Roy,
G.Verkhivker,
J.S.Laurence,
C.R.Middaugh,
and
T.J.Siahaan
(2009).
The role of covalent dimerization on the physical and chemical stability of the EC1 domain of human E-cadherin.
|
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J Pharm Sci,
98,
3562-3574.
|
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M.Yokouchi,
M.A.Saleh,
K.Kuroda,
T.Hachiya,
J.R.Stanley,
M.Amagai,
and
K.Ishii
(2009).
Pathogenic epitopes of autoantibodies in pemphigus reside in the amino-terminal adhesive region of desmogleins which are unmasked by proteolytic processing of prosequence.
|
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J Invest Dermatol,
129,
2156-2166.
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P.Hulpiau,
and
F.van Roy
(2009).
Molecular evolution of the cadherin superfamily.
|
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Int J Biochem Cell Biol,
41,
349-369.
|
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P.Katsamba,
K.Carroll,
G.Ahlsen,
F.Bahna,
J.Vendome,
S.Posy,
M.Rajebhosale,
S.Price,
T.M.Jessell,
A.Ben-Shaul,
L.Shapiro,
and
B.H.Honig
(2009).
Linking molecular affinity and cellular specificity in cadherin-mediated adhesion.
|
| |
Proc Natl Acad Sci U S A,
106,
11594-11599.
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R.M.Harmon,
B.V.Desai,
and
K.J.Green
(2009).
Regulatory roles of the cadherin superfamily.
|
| |
F1000 Biol Rep,
1,
0.
|
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S.H.Lim,
S.K.Kwon,
M.K.Lee,
J.Moon,
D.G.Jeong,
E.Park,
S.J.Kim,
B.C.Park,
S.C.Lee,
S.E.Ryu,
D.Y.Yu,
B.H.Chung,
E.Kim,
P.K.Myung,
and
J.R.Lee
(2009).
Synapse formation regulated by protein tyrosine phosphatase receptor T through interaction with cell adhesion molecules and Fyn.
|
| |
EMBO J,
28,
3564-3578.
|
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Y.Li,
M.Hofmann,
Q.Wang,
L.Teng,
L.K.Chlewicki,
H.Pircher,
and
R.A.Mariuzza
(2009).
Structure of natural killer cell receptor KLRG1 bound to E-cadherin reveals basis for MHC-independent missing self recognition.
|
| |
Immunity,
31,
35-46.
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PDB codes:
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Y.Zhang,
S.Sivasankar,
W.J.Nelson,
and
S.Chu
(2009).
Resolving cadherin interactions and binding cooperativity at the single-molecule level.
|
| |
Proc Natl Acad Sci U S A,
106,
109-114.
|
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Y.Zhang,
Y.Zhou,
J.Zhu,
S.Dong,
C.Li,
and
Q.Xiang
(2009).
Effect of a novel recombinant protein of fibronectinIII7-10/cadherin 11 EC1-2 on osteoblastic adhesion and differentiation.
|
| |
Biosci Biotechnol Biochem,
73,
1999-2006.
|
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C.Y.Tai,
S.A.Kim,
and
E.M.Schuman
(2008).
Cadherins and synaptic plasticity.
|
| |
Curr Opin Cell Biol,
20,
567-575.
|
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|
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D.Studer,
B.M.Humbel,
and
M.Chiquet
(2008).
Electron microscopy of high pressure frozen samples: bridging the gap between cellular ultrastructure and atomic resolution.
|
| |
Histochem Cell Biol,
130,
877-889.
|
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|
|
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J.M.Benjamin,
and
W.J.Nelson
(2008).
Bench to bedside and back again: molecular mechanisms of alpha-catenin function and roles in tumorigenesis.
|
| |
Semin Cancer Biol,
18,
53-64.
|
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J.S.Yu,
S.Koujak,
S.Nagase,
C.M.Li,
T.Su,
X.Wang,
M.Keniry,
L.Memeo,
A.Rojtman,
M.Mansukhani,
H.Hibshoosh,
B.Tycko,
and
R.Parsons
(2008).
PCDH8, the human homolog of PAPC, is a candidate tumor suppressor of breast cancer.
|
| |
Oncogene,
27,
4657-4665.
|
|
|
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L.Tabernero,
A.R.Aricescu,
E.Y.Jones,
and
S.E.Szedlacsek
(2008).
Protein tyrosine phosphatases: structure-function relationships.
|
| |
FEBS J,
275,
867-882.
|
|
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|
|
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M.P.Stemmler
(2008).
Cadherins in development and cancer.
|
| |
Mol Biosyst,
4,
835-850.
|
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PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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only a partial list as not all journals are covered by
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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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