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Cell adhesion, metal binding protein PDB-id
1l3w
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Description
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PROCHECK
Protein chain
540 a.a. *
Ligands
NAG ×11
NDG ×4
Metal ions
_CA ×12
Waters ×38

* Residue conservation analysis
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PDB id: 1l3w
Name: Cell adhesion, metal binding protein
Title: C-cadherin ectodomain

Structure:
Ep-cadherin. Chain: a. Fragment: c-cadherin ectodomain. Synonym: c-cadherin. Engineered: yes

Source:
Xenopus laevis. African clawed frog. Organism_taxid: 8355. Expressed in: cricetulus griseus. Expression_system_taxid: 10029. Expression_system_tissue: secretion. Expression_system_cell: choki cells.

UniProt:
P33148 (CADHF_XENLA) Pfam   ArchSchema ?
Seq:
Struc:
Seq:
Struc:
Seq:
Struc:
Seq: 880 a.a.
Struc: 540 a.a.
Key:    PfamA domain
 Secondary structure  CATH domain

Resolution:
3.08Å

R-factor:
0.243

R-free:
0.276

Authors:
T.J.Boggon,J.Murray,S.Chappuis-Flament,E.Wong,B.M.Gumbiner, L.Shapiro

Key ref:
T.J.Boggon et al. (2002). C-cadherin ectodomain structure and implications for cell adhesion mechanisms.. Science, 296, 1308-1313. [PubMed id: 11964443] [DOI: 10.1126/science.1071559]

Date:
01-Mar-02

Release date:
26-Apr-02

Related entries:
1ncg
n-cadherin 1-domain crystal structure
1nch
n-cadherin 1-domain crystal structure
1nci
n-cadherin 1-domain crystal structure
1edh
e-cadherin 2-domain crystal structure
1ff5
e-cadherin 2-domain crystal structure
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    Key reference    
 
 
DOI no: 10.1126/science.1071559 Science 296:1308-1313 (2002)
PubMed id: 11964443  
 
 
C-cadherin ectodomain structure and implications for cell adhesion mechanisms.
T.J.Boggon, J.Murray, S.Chappuis-Flament, E.Wong, B.M.Gumbiner, L.Shapiro.
 
  ABSTRACT  
 
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.
 
  Selected figure(s)  
 
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).
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).
 
  The above figures are reprinted by permission from the AAAs: Science (2002, 296, 1308-1313) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19302290 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.
  Cancer Sci, 100, 888-895.  
19680686 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.
  Virchows Arch, 455, 245-251.  
19948502 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.
  J Cell Biol, 187, 553-567.  
19635050 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.
  Chem Biol Drug Des, 73, 584-598.  
  20066110 L.Shapiro, and W.I.Weis (2009).
Structure and biochemistry of cadherins and catenins.
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19076794 M.Jelani, M.Salman Chishti, and W.Ahmad (2009).
A novel splice-site mutation in the CDH3 gene in hypotrichosis with juvenile macular dystrophy.
  Clin Exp Dermatol, 34, 68-73.  
19199298 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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19553217 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.  
19816407 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.  
19114658 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.  
19734674 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.  
18795316 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.  
18408767 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.  
18298793 L.Tabernero, A.R.Aricescu, E.Y.Jones, and S.E.Szedlacsek (2008).
Protein tyrosine phosphatases: structure-function relationships.
  FEBS J, 275, 867-882.  
18633485 M.P.Stemmler (2008).
Cadherins in development and cancer.
  Mol Biosyst, 4, 835-850.  
18326636 M.Sotomayor, and K.Schulten (2008).
The allosteric role of the Ca2+ switch in adhesion and elasticity of C-cadherin.
  Biophys J, 94, 4621-4633.  
18552401 Q.Shi, Y.H.Chien, and D.Leckband (2008).
Biophysical properties of cadherin bonds do not predict cell sorting.
  J Biol Chem, 283, 28454-28463.  
18343874 S.Bibert, H.Ayari, D.Riveline, E.Concord, B.Hermant, T.Vernet, and D.Gulino-Debrac (2008).
Establishment of cell-cell junctions depends on the oligomeric states of VE-cadherin.
  J Biochem, 143, 821-832.  
18064004 A.Al-Amoudi, D.C.Díez, M.J.Betts, and A.S.Frangakis (2007).
The molecular architecture of cadherins in native epidermal desmosomes.
  Nature, 450, 832-837.  
17761881 A.R.Aricescu, C.Siebold, K.Choudhuri, V.T.Chang, W.Lu, S.J.Davis, P.A.van der Merwe, and E.Y.Jones (2007).
Structure of a tyrosine phosphatase adhesive interaction reveals a spacer-clamp mechanism.
  Science, 317, 1217-1220.
PDB code: 2v5y
17093058 C.T.Capaldo, and I.G.Macara (2007).
Depletion of E-cadherin disrupts establishment but not maintenance of cell junctions in Madin-Darby canine kidney epithelial cells.
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17496052 E.H.Lee, J.Hsin, O.Mayans, and K.Schulten (2007).
Secondary and tertiary structure elasticity of titin Z1Z2 and a titin chain model.
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17397555 L.Daugaard, L.O.Andresen, and M.Fredholm (2007).
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17600523 L.Shapiro, J.Love, and D.R.Colman (2007).
Adhesion molecules in the nervous system: structural insights into function and diversity.
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17342797 M.Indelman, J.Eason, M.Hummel, O.Loza, M.Suri, M.J.Leys, M.Bayne, F.L.Schwartz, and E.Sprecher (2007).
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  Clin Exp Dermatol, 32, 191-196.  
18045497 M.J.Harrington, E.Hong, O.Fasanmi, and R.Brewster (2007).
Cadherin-mediated adhesion regulates posterior body formation.
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17805295 P.Kazmierczak, H.Sakaguchi, J.Tokita, E.M.Wilson-Kubalek, R.A.Milligan, U.Müller, and B.Kachar (2007).
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  Nature, 449, 87-91.  
17761538 R.B.Troyanovsky, O.Laur, and S.M.Troyanovsky (2007).
Stable and unstable cadherin dimers: mechanisms of formation and roles in cell adhesion.
  Mol Biol Cell, 18, 4343-4352.  
17539752 S.Pokutta, and W.I.Weis (2007).
Structure and mechanism of cadherins and catenins in cell-cell contacts.
  Annu Rev Cell Dev Biol, 23, 237-261.  
17715295 T.Wollert, D.W.Heinz, and W.D.Schubert (2007).
Thermodynamically reengineering the listerial invasion complex InlA/E-cadherin.
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PDB codes: 2omt 2omu 2omx 2omz
17881562 X.Chen, T.D.Kim, C.V.Carman, L.Z.Mi, G.Song, and T.A.Springer (2007).
Structural plasticity in Ig superfamily domain 4 of ICAM-1 mediates cell surface dimerization.
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PDB code: 2oz4
17023539 A.K.Prakasam, V.Maruthamuthu, and D.E.Leckband (2006).
Similarities between heterophilic and homophilic cadherin adhesion.
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16440298 A.M.Elste, and D.L.Benson (2006).
Structural basis for developmentally regulated changes in cadherin function at synapses.
  J Comp Neurol, 495, 324-335.  
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Force-dependent chemical kinetics of disulfide bond reduction observed with single-molecule techniques.
  Proc Natl Acad Sci U S A, 103, 7222-7227.  
16287100 A.Prasad, H.Zhao, J.M.Rutherford, N.Housley, C.Nichols, and S.Pedigo (2006).
Effect of linker segments on the stability of epithelial cadherin Domain 2.
  Proteins, 62, 111-121.  
16407198 B.O.Smith, N.C.Picken, G.D.Westrop, K.Bromek, J.C.Mottram, and G.H.Coombs (2006).
The structure of Leishmania mexicana ICP provides evidence for convergent evolution of cysteine peptidase inhibitors.
  J Biol Chem, 281, 5821-5828.
PDB code: 2c34
16834557 D.Leckband, and A.Prakasam (2006).
Mechanism and dynamics of cadherin adhesion.
  Annu Rev Biomed Eng, 8, 259-287.  
16980367 F.Cailliez, and R.Lavery (2006).
Dynamics and stability of E-cadherin dimers.
  Biophys J, 91, 3964-3971.  
16841036 H.Kawasaki, K.Tsunoda, T.Hata, K.Ishii, T.Yamada, and M.Amagai (2006).
Synergistic pathogenic effects of combined mouse monoclonal anti-desmoglein 3 IgG antibodies on pemphigus vulgaris blister formation.
  J Invest Dermatol, 126, 2621-2630.  
16543896 J.V.Schaffer, H.Bazzi, A.Vitebsky, A.Witkiewicz, O.I.Kovich, H.Kamino, L.S.Shapiro, S.P.Amin, S.J.Orlow, and A.M.Christiano (2006).
Mutations in the desmoglein 4 gene underlie localized autosomal recessive hypotrichosis with monilethrix hairs and congenital scalp erosions.
  J Invest Dermatol, 126, 1286-1291.  
17075192 M.Amagai (2006).
[Desmoglein, the target molecule in autoimmunity and infection]
  Nihon Rinsho Meneki Gakkai Kaishi, 29, 325-333.  
16896432 M.Gao, M.Sotomayor, E.Villa, E.H.Lee, and K.Schulten (2006).
Molecular mechanisms of cellular mechanics.
  Phys Chem Chem Phys, 8, 3692-3706.  
16326909 M.V.Bayas, A.Leung, E.Evans, and D.Leckband (2006).
Lifetime measurements reveal kinetic differences between homophilic cadherin bonds.
  Biophys J, 90, 1385-1395.  
16319177 O.Thoumine, M.Lambert, R.M.Mège, and D.Choquet (2006).
Regulation of N-cadherin dynamics at neuronal contacts by ligand binding and cytoskeletal coupling.
  Mol Biol Cell, 17, 862-875.  
16770573 P.John, M.Tariq, M.Arshad Rafiq, M.Amin-Ud-Din, D.Muhammad, I.Waheed, M.Ansar, and W.Ahmad (2006).
Recurrent intragenic deletion mutation in desmoglein 4 gene underlies autosomal recessive hypotrichosis in two Pakistani families of Balochi and Sindhi origins.
  Arch Dermatol Res, 298, 135-137.  
16760429 R.B.Troyanovsky, E.P.Sokolov, and S.M.Troyanovsky (2006).
Endocytosis of cadherin from intracellular junctions is the driving force for cadherin adhesive dimer disassembly.
  Mol Biol Cell, 17, 3484-3493.  
17057715 Z.Lin, S.Sriskanthadevan, H.Huang, C.H.Siu, and D.Yang (2006).
Solution structures of the adhesion molecule DdCAD-1 reveal new insights into Ca(2+)-dependent cell-cell adhesion.
  Nat Struct Mol Biol, 13, 1016-1022.
PDB codes: 1yhp 2b1o
16297213 A.G.Messenger, H.Bazzi, R.Parslew, L.Shapiro, and A.M.Christiano (2005).
A missense mutation in the cadherin interaction site of the desmoglein 4 gene underlies localized autosomal recessive hypotrichosis.
  J Invest Dermatol, 125, 1077-1079.  
16030252 A.M.Shewan, M.Maddugoda, A.Kraemer, S.J.Stehbens, S.Verma, E.M.Kovacs, and A.S.Yap (2005).
Myosin 2 is a key Rho kinase target necessary for the local concentration of E-cadherin at cell-cell contacts.
  Mol Biol Cell, 16, 4531-4542.  
16025097 B.M.Gumbiner (2005).
Regulation of cadherin-mediated adhesion in morphogenesis.
  Nat Rev Mol Cell Biol, 6, 622-634.  
15937105 C.P.Chen, S.Posy, A.Ben-Shaul, L.Shapiro, and B.H.Honig (2005).
Specificity of cell-cell adhesion by classical cadherins: Critical role for low-affinity dimerization through beta-strand swapping.
  Proc Natl Acad Sci U S A, 102, 8531-8536.  
16183887 F.Cailliez, and R.Lavery (2005).
Cadherin mechanics and complexation: the importance of calcium binding.
  Biophys J, 89, 3895-3903.  
16382669 H.Bazzi, A.Martinez-Mir, A.Kljuic, and A.M.Christiano (2005).
Desmoglein 4 mutations underlie localized autosomal recessive hypotrichosis in humans, mice, and rats.
  J Investig Dermatol Symp Proc, 10, 222-224.  
15743489 H.P.Kiener, and M.B.Brenner (2005).
Building the synovium: cadherin-11 mediates fibroblast-like synoviocyte cell-to-cell adhesion.
  Arthritis Res Ther, 7, 49-54.  
16238811 K.Nishifuji, Y.Fudaba, T.Yamaguchi, T.Iwasaki, M.Sugai, and M.Amagai (2005).
Cloning of swine desmoglein 1 and its direct proteolysis by Staphylococcus hyicus exfoliative toxins isolated from pigs with exudative epidermitis.
  Vet Dermatol, 16, 315-323.  
15805154 K.W.Kjaer, L.Hansen, G.C.Schwabe, A.P.Marques-de-Faria, H.Eiberg, S.Mundlos, N.Tommerup, and T.Rosenberg (2005).
Distinct CDH3 mutations cause ectodermal dysplasia, ectrodactyly, macular dystrophy (EEM syndrome).
  J Med Genet, 42, 292-298.  
16041761 P.C.Salinas (2005).
Signaling at the vertebrate synapse: new roles for embryonic morphogens?
  J Neurobiol, 64, 435-445.  
15744052 Q.Wu (2005).
Comparative genomics and diversifying selection of the clustered vertebrate protocadherin genes.
  Genetics, 169, 2179-2188.  
15554942 A.Schambony, M.Kunz, and D.Gradl (2004).
Cross-regulation of Wnt signaling and cell adhesion.
  Differentiation, 72, 307-318.  
15617564 B.Meyer, H.Bazzi, V.Zidek, A.Musilova, M.Pravenec, T.W.Kurtz, P.Nurnberg, and A.M.Christiano (2004).
A spontaneous mutation in the desmoglein 4 gene underlies hypotrichosis in a new lanceolate hair rat model.
  Differentiation, 72, 541-547.  
15304105 C.Moss, A.Martinez-Mir, H.Lam, M.Tadin-Strapps, A.Kljuic, and A.M.Christiano (2004).
A recurrent intragenic deletion in the desmoglein 4 gene underlies localized autosomal recessive hypotrichosis.
  J Invest Dermatol, 123, 607-610.  
15071499 D.Häussinger, T.Ahrens, T.Aberle, J.Engel, J.Stetefeld, and S.Grzesiek (2004).
Proteolytic E-cadherin activation followed by solution NMR and X-ray crystallography.
  EMBO J, 23, 1699-1708.
PDB code: 1q1p
15546992 E.Perret, A.Leung, H.Feracci, and E.Evans (2004).
Trans-bonded pairs of E-cadherin exhibit a remarkable hierarchy of mechanical strengths.
  Proc Natl Acad Sci U S A, 101, 16472-16477.  
15606503 H.Bazzi, A.Kljuic, A.M.Christiano, A.M.Christiano, and A.A.Panteleyev (2004).
Intragenic deletion in the Desmoglein 4 gene underlies the skin phenotype in the Iffa Credo "hairless" rat.
  Differentiation, 72, 450-464.  
15112230 J.M.Gooding, K.L.Yap, and M.Ikura (2004).
The cadherin-catenin complex as a focal point of cell adhesion and signalling: new insights from three-dimensional structures.
  Bioessays, 26, 497-511.  
15057245 J.Siemens, C.Lillo, R.A.Dumont, A.Reynolds, D.S.Williams, P.G.Gillespie, and U.Müller (2004).
Cadherin 23 is a component of the tip link in hair-cell stereocilia.
  Nature, 428, 950-955.  
15259055 M.Fuchs, P.Hutzler, G.Handschuh, C.Hermannstädter, I.Brunner, H.Höfler, and B.Luber (2004).
Dynamics of cell adhesion and motility in living cells is altered by a single amino acid change in E-cadherin fused to enhanced green fluorescent protein.
  Cell Motil Cytoskeleton, 59, 50-61.  
15609097 M.Goodwin, and A.S.Yap (2004).
Classical cadherin adhesion molecules: coordinating cell adhesion, signaling and the cytoskeleton.
  J Mol Histol, 35, 839-844.  
15071552 S.Getsios, A.C.Huen, and K.J.Green (2004).
Working out the strength and flexibility of desmosomes.
  Nat Rev Mol Cell Biol, 5, 271-281.  
15606501 S.Getsios, E.V.Amargo, R.L.Dusek, K.Ishii, L.Sheu, L.M.Godsel, and K.J.Green (2004).
Coordinated expression of desmoglein 1 and desmocollin 1 regulates intercellular adhesion.
  Differentiation, 72, 419-433.  
15165472 T.A.Brieva, and P.V.Moghe (2004).
Engineering the hepatocyte differentiation-proliferation balance by acellular cadherin micropresentation.
  Tissue Eng, 10, 553-564.  
14748083 T.A.Brieva, and P.V.Moghe (2004).
Exogenous cadherin microdisplay can interfere with endogenous signaling and reprogram gene expression in cultured hepatocytes.
  Biotechnol Bioeng, 85, 283-292.  
  15545999 T.Nagasaka, K.Nishifuji, T.Ota, N.V.Whittock, and M.Amagai (2004).
Defining the pathogenic involvement of desmoglein 4 in pemphigus and staphylococcal scalded skin syndrome.
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15377520 V.Tsuprun, R.J.Goodyear, and G.P.Richardson (2004).
The structure of tip links and kinocilial links in avian sensory hair bundles.
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15057284 X.Qian, T.Karpova, A.M.Sheppard, J.McNally, and D.R.Lowy (2004).
E-cadherin-mediated adhesion inhibits ligand-dependent activation of diverse receptor tyrosine kinases.
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12770907 B.Zhu, S.Chappuis-Flament, E.Wong, I.E.Jensen, B.M.Gumbiner, and D.Leckband (2003).
Functional analysis of the structural basis of homophilic cadherin adhesion.
  Biophys J, 84, 4033-4042.  
14570569 M.J.Wheelock, and K.R.Johnson (2003).
Cadherins as modulators of cellular phenotype.
  Annu Rev Cell Dev Biol, 19, 207-235.  
14585958 R.B.Troyanovsky, E.Sokolov, and S.M.Troyanovsky (2003).
Adhesive and lateral E-cadherin dimers are mediated by the same interface.
  Mol Cell Biol, 23, 7965-7972.  
12880431 Y.Hanakawa, T.Selwood, D.Woo, C.Lin, N.M.Schechter, and J.R.Stanley (2003).
Calcium-dependent conformation of desmoglein 1 is required for its cleavage by exfoliative toxin.
  J Invest Dermatol, 121, 383-389.  
12786748 Z.M.Ahmed, S.Riazuddin, S.Riazuddin, and E.R.Wilcox (2003).
The molecular genetics of Usher syndrome.
  Clin Genet, 63, 431-444.  
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.