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(-) Description

Title :  S-SHAPED TRANS INTERACTIONS OF CADHERINS MODEL BASED ON FITTING C-CADHERIN (1L3W) TO 3D MAP OF DESMOSOMES OBTAINED BY ELECTRON TOMOGRAPHY
 
Authors :  W. He, P. Cowin, D. L. Stokes
Date :  06 Aug 03  (Deposition) - 07 Oct 03  (Release) - 13 Jul 11  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  30.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cadherin; Trans Interaction; Desmosome; Junction; Adhesion, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. He, P. Cowin, D. L. Stokes
Untangling Desmosomal Knots With Electron Tomography
Science V. 302 109 2003
PubMed-ID: 14526082  |  Reference-DOI: 10.1126/SCIENCE.1086957

(-) Compounds

Molecule 1 - EP-CADHERIN
    Chains: A, B
    Fragment: RESIDUES 1-546 OF PDB ENTRY 1L3W
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: RIGID BODY FIT BY C-CADHERIN FROM PDB ENTRY 1L3W
    Other Details - Source: DESMOSOME PREPARATION FROM NEWBORN MOUSE SKIN
    Synonym: C-CADHERIN
    Tissue: SKIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 54)

Asymmetric/Biological Unit (3, 54)
No.NameCountTypeFull Name
1CA24Ligand/IonCALCIUM ION
2NAG22Ligand/IonN-ACETYL-D-GLUCOSAMINE
3NDG8Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (54, 54)

Asymmetric Unit (54, 54)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:154 , PRO A:155 , GLU A:186 , TYR A:187 , THR A:188BINDING SITE FOR RESIDUE NAG A 801
02AC2SOFTWAREASP A:222 , THR A:245BINDING SITE FOR RESIDUE NAG A 802
03AC3SOFTWAREGLN A:256 , VAL A:258 , TYR A:259 , ILE A:271 , THR A:272 , THR A:273BINDING SITE FOR RESIDUE NAG A 803
04AC4SOFTWAREPHE A:308 , LEU A:312 , THR A:314BINDING SITE FOR RESIDUE NDG A 804
05AC5SOFTWARETHR A:301 , THR A:314 , THR A:316 , NAG A:806BINDING SITE FOR RESIDUE NAG A 805
06AC6SOFTWARELYS A:224 , THR A:225 , GLN A:299 , THR A:316 , THR A:318 , NAG A:805BINDING SITE FOR RESIDUE NAG A 806
07AC7SOFTWARETHR A:227 , VAL A:297 , THR A:320BINDING SITE FOR RESIDUE NAG A 807
08AC8SOFTWARELYS A:402 , TYR A:406 , THR A:407BINDING SITE FOR RESIDUE NAG A 808
09AC9SOFTWARELEU A:411 , VAL A:419 , GLY A:420 , THR A:421 , NAG A:810BINDING SITE FOR RESIDUE NAG A 809
10BC1SOFTWARETHR A:421 , THR A:423 , NAG A:809 , NDG A:811BINDING SITE FOR RESIDUE NAG A 810
11BC2SOFTWAREALA A:335 , ILE A:409 , THR A:425 , NAG A:810BINDING SITE FOR RESIDUE NDG A 811
12BC3SOFTWARETYR A:226 , THR A:227 , ALA A:228 , GLN A:240BINDING SITE FOR RESIDUE NAG A 812
13BC4SOFTWAREASN A:403BINDING SITE FOR RESIDUE NDG A 902
14BC5SOFTWAREASN A:270BINDING SITE FOR RESIDUE NDG A 903
15BC6SOFTWAREVAL A:524 , ASN A:526BINDING SITE FOR RESIDUE NAG A 904
16BC7SOFTWAREASP B:154 , PRO B:155 , GLU B:186 , TYR B:187 , THR B:188BINDING SITE FOR RESIDUE NAG B 801
17BC8SOFTWAREASP B:222 , THR B:245BINDING SITE FOR RESIDUE NAG B 802
18BC9SOFTWAREGLN B:256 , VAL B:258 , TYR B:259 , ILE B:271 , THR B:272 , THR B:273BINDING SITE FOR RESIDUE NAG B 803
19CC1SOFTWAREPHE B:308 , LEU B:312 , THR B:314BINDING SITE FOR RESIDUE NDG B 804
20CC2SOFTWARETHR B:301 , THR B:314 , THR B:316 , NAG B:806BINDING SITE FOR RESIDUE NAG B 805
21CC3SOFTWARELYS B:224 , THR B:225 , GLN B:299 , THR B:316 , THR B:318 , NAG B:805BINDING SITE FOR RESIDUE NAG B 806
22CC4SOFTWARETHR B:227 , VAL B:297 , THR B:320BINDING SITE FOR RESIDUE NAG B 807
23CC5SOFTWARELYS B:402 , TYR B:406 , THR B:407BINDING SITE FOR RESIDUE NAG B 808
24CC6SOFTWARELEU B:411 , VAL B:419 , GLY B:420 , THR B:421 , NAG B:810BINDING SITE FOR RESIDUE NAG B 809
25CC7SOFTWARETHR B:421 , THR B:423 , NAG B:809 , NDG B:811BINDING SITE FOR RESIDUE NAG B 810
26CC8SOFTWAREALA B:335 , ILE B:409 , THR B:425 , NAG B:810BINDING SITE FOR RESIDUE NDG B 811
27CC9SOFTWARETYR B:226 , THR B:227 , ALA B:228 , GLN B:240BINDING SITE FOR RESIDUE NAG B 812
28DC1SOFTWAREASN B:403BINDING SITE FOR RESIDUE NDG B 902
29DC2SOFTWAREASN B:270BINDING SITE FOR RESIDUE NDG B 903
30DC3SOFTWAREVAL B:524 , ASN B:526BINDING SITE FOR RESIDUE NAG B 904
31DC4SOFTWAREASN A:102 , ASN A:104 , ASP A:134 , ASP A:136 , ASN A:143 , ASP A:195BINDING SITE FOR RESIDUE CA A 905
32DC5SOFTWAREGLU A:11 , GLU A:69 , ASP A:100 , GLN A:101 , ASP A:103 , ASP A:136BINDING SITE FOR RESIDUE CA A 906
33DC6SOFTWAREGLU A:11 , ASN A:12 , ASP A:67 , GLU A:69 , ASP A:103BINDING SITE FOR RESIDUE CA A 907
34DC7SOFTWAREGLU A:119 , GLU A:182 , ASP A:213 , ALA A:214 , ASP A:216 , ASP A:248BINDING SITE FOR RESIDUE CA A 908
35DC8SOFTWAREGLU A:119 , ASP A:180 , GLU A:182 , ASP A:216BINDING SITE FOR RESIDUE CA A 909
36DC9SOFTWAREASN A:215 , ASN A:217 , ASP A:246 , ASP A:248 , ALA A:254 , ASN A:304BINDING SITE FOR RESIDUE CA A 910
37EC1SOFTWAREGLU A:232 , ASP A:289 , GLU A:291 , GLU A:328 , CA A:915BINDING SITE FOR RESIDUE CA A 911
38EC2SOFTWAREASN A:327 , GLU A:328 , ASP A:358 , ASP A:360 , GLN A:365 , ASP A:414BINDING SITE FOR RESIDUE CA A 912
39EC3SOFTWAREGLU A:343 , ASP A:395 , GLU A:397 , ASP A:435 , CA A:916BINDING SITE FOR RESIDUE CA A 913
40EC4SOFTWAREASN A:434 , ASN A:436 , ASP A:461 , ASP A:463 , ASN A:467 , ASP A:515BINDING SITE FOR RESIDUE CA A 914
41EC5SOFTWAREGLU A:232 , GLU A:291 , ASP A:325 , VAL A:326 , GLU A:328 , ASP A:360 , CA A:911BINDING SITE FOR RESIDUE CA A 915
42EC6SOFTWAREGLU A:343 , GLU A:397 , ASP A:432 , VAL A:433 , ASP A:435 , ASP A:463 , CA A:913BINDING SITE FOR RESIDUE CA A 916
43EC7SOFTWAREASN B:102 , ASN B:104 , ASP B:134 , ASP B:136 , ASN B:143 , ASP B:195BINDING SITE FOR RESIDUE CA B 905
44EC8SOFTWAREGLU B:11 , GLU B:69 , ASP B:100 , GLN B:101 , ASP B:103 , ASP B:136BINDING SITE FOR RESIDUE CA B 906
45EC9SOFTWAREGLU B:11 , ASN B:12 , ASP B:67 , GLU B:69 , ASP B:103BINDING SITE FOR RESIDUE CA B 907
46FC1SOFTWAREGLU B:119 , GLU B:182 , ASP B:213 , ALA B:214 , ASP B:216 , ASP B:248BINDING SITE FOR RESIDUE CA B 908
47FC2SOFTWAREGLU B:119 , ASP B:180 , GLU B:182 , ASP B:216BINDING SITE FOR RESIDUE CA B 909
48FC3SOFTWAREASN B:215 , ASN B:217 , ASP B:246 , ASP B:248 , ALA B:254 , ASN B:304BINDING SITE FOR RESIDUE CA B 910
49FC4SOFTWAREGLU B:232 , ASP B:289 , GLU B:291 , GLU B:328 , CA B:915BINDING SITE FOR RESIDUE CA B 911
50FC5SOFTWAREASN B:327 , GLU B:328 , ASP B:358 , ASP B:360 , GLN B:365 , ASP B:414BINDING SITE FOR RESIDUE CA B 912
51FC6SOFTWAREGLU B:343 , ASP B:395 , GLU B:397 , ASP B:435 , CA B:916BINDING SITE FOR RESIDUE CA B 913
52FC7SOFTWAREASN B:434 , ASN B:436 , ASP B:461 , ASP B:463 , ASN B:467 , ASP B:515BINDING SITE FOR RESIDUE CA B 914
53FC8SOFTWAREGLU B:232 , GLU B:291 , ASP B:325 , VAL B:326 , GLU B:328 , ASP B:360 , CA B:911BINDING SITE FOR RESIDUE CA B 915
54FC9SOFTWAREGLU B:343 , GLU B:397 , ASP B:432 , VAL B:433 , ASP B:435 , ASP B:463 , CA B:913BINDING SITE FOR RESIDUE CA B 916

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:448 -A:532
2A:530 -A:539
3B:448 -B:532
4B:530 -B:539

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Phe A:17 -Pro A:18
2Pro A:46 -Pro A:47
3Glu A:157 -Pro A:158
4Pro A:465 -Pro A:466
5Phe B:17 -Pro B:18
6Pro B:46 -Pro B:47
7Glu B:157 -Pro B:158
8Pro B:465 -Pro B:466

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q5A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q5A)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q5A)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:540
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d1q5aa_ A: Ep-cadherin                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee........eeeee...hhhhh..eeeeeee..........eee.....eeee..........eeeeeeeeee.........eeeeeeee.......ee....eeeeee......eeeee..ee...............eeeee.........eee.....eeee...........eeeeeeeeehhhhh..eee..eeeeee............eeeeeee......eeeee..............ee..........eeeee......eeeee...........eeeee..ee............eeeeeeee......ee...ee...........eeeee..ee.........eeeee........eee....eeee................eeeeeeee.........eeee...........ee....eee.......eeeeee................................eeee.............eee........eeee..eee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1q5a A   1 DWVIPPIKVSENERGPFPKRLVQIKSNKDRFNKVYYSITGQGADNPPQGVFRIEWETGWMLVTRPLDREEYDKYVLSSHAVSENGSPVEEPMEITINVIDQNDNRPKFTQDVFRGSVREGVQPGTQVMAVSATDEDDNIDSLNGVLSYSILKQDPEEPIPNLFTINRETGVISLIGTGLDREKFPEYTLTVQATDLEGAGLSVEGKAIIQITDANDNAPIFDPKTYTALVPENEIGFEVQRLSVTDLDMPGTPAWQAVYKIRVNEGGFFNITTDPESNQGILTTAKGLDFELRKQYVLQITVENAEPFSVPLPTSTATVTVTVEDVNEAPFFVPAVSRVDVSEDLSRGEKIISLVAQDPDKQQIQKLSYFIGNDPARWLTVNKDNGIVTGNGNLDRESEYVKNNTYTVIMLVTDDGVSVGTGTGTLILHVLDVNDNGPVPSPRVFTMCDQNPEPQVLTISDADIPPNTYPYKVSLSHGSDLTWKAELDSKGTSMLLSPTQQLKKGDYSIYVLLSDAQNNPQLTVVNATVCSCEGKAIKCQ 540
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540


Chain B from PDB  Type:PROTEIN  Length:540
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d1q5ab_ B: Ep-cadherin                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee........eeeee...hhhhh..eeeeeee..........eee.....eeee..........eeeeeeeeee.........eeeeeeee.......ee....eeeeee......eeeee..ee...............eeeee.........eee.....eeee...........eeeeeeeeehhhhh..eee..eeeeee............eeeeeee......eeeee..............ee..........eeeee......eeeee...........eeeee..ee............eeeeeeee......ee...ee...........eeeee..ee.........eeeee........eee....eeee................eeeeeeee.........eeee...........ee....eee.......eeeeee................................eeee.............eee........eeee..eee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1q5a B   1 DWVIPPIKVSENERGPFPKRLVQIKSNKDRFNKVYYSITGQGADNPPQGVFRIEWETGWMLVTRPLDREEYDKYVLSSHAVSENGSPVEEPMEITINVIDQNDNRPKFTQDVFRGSVREGVQPGTQVMAVSATDEDDNIDSLNGVLSYSILKQDPEEPIPNLFTINRETGVISLIGTGLDREKFPEYTLTVQATDLEGAGLSVEGKAIIQITDANDNAPIFDPKTYTALVPENEIGFEVQRLSVTDLDMPGTPAWQAVYKIRVNEGGFFNITTDPESNQGILTTAKGLDFELRKQYVLQITVENAEPFSVPLPTSTATVTVTVEDVNEAPFFVPAVSRVDVSEDLSRGEKIISLVAQDPDKQQIQKLSYFIGNDPARWLTVNKDNGIVTGNGNLDRESEYVKNNTYTVIMLVTDDGVSVGTGTGTLILHVLDVNDNGPVPSPRVFTMCDQNPEPQVLTISDADIPPNTYPYKVSLSHGSDLTWKAELDSKGTSMLLSPTQQLKKGDYSIYVLLSDAQNNPQLTVVNATVCSCEGKAIKCQ 540
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Low resolution protein structures (283)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Q5A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Q5A)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1Q5A)

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  1q5a
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

1l3w C-CADHERIN ECTODOMAIN
1q55
1q5b
1q5c RELATED ID: EMD-1052 RELATED DB: EMDB