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(-) Description

Title :  CRYSTAL STRUCTURE OF CHICKEN VE-CADHERIN EC1-2
 
Authors :  J. Brasch, O. J. Harrison, G. Ahlsen, S. M. Carnally, R. M. Henderson, B. L. S. Shapiro
Date :  24 Nov 10  (Deposition) - 02 Feb 11  (Release) - 20 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Extracellular Cadherin (Ec) Domain, Beta Barrel, Ig-Domain Like, Domain Swapped Dimer Interface, Calcium Dependent Cell-Cell Adhesion, Cell Surface, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Brasch, O. J. Harrison, G. Ahlsen, S. M. Carnally, R. M. Henderson, B. Honig, L. Shapiro
Structure And Binding Mechanism Of Vascular Endothelial Cadherin: A Divergent Classical Cadherin.
J. Mol. Biol. V. 408 57 2011
PubMed-ID: 21269602  |  Reference-DOI: 10.1016/J.JMB.2011.01.031

(-) Compounds

Molecule 1 - VASCULAR ENDOTHELIAL CADHERIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPSMT3
    Expression System StrainROSETTA2DE3 PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCHICKEN VE-CADHERIN DOMAINS EC1-EC2, UNP RESIDUES 41-243
    Organism CommonBANTAM,CHICKENS
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:11 , GLU A:12 , ASP A:62 , GLU A:64 , ASP A:99 , HOH A:311BINDING SITE FOR RESIDUE CA A 401
2AC2SOFTWAREASN A:98 , ASN A:100 , ASP A:130 , ASP A:132 , HIS A:139 , ASP A:184BINDING SITE FOR RESIDUE CA A 402
3AC3SOFTWAREGLU A:11 , GLU A:64 , ASP A:96 , ILE A:97 , ASP A:99 , ASP A:132BINDING SITE FOR RESIDUE CA A 403
4AC4SOFTWAREGLU B:11 , GLU B:12 , ASP B:62 , GLU B:64 , ASP B:99 , HOH B:343BINDING SITE FOR RESIDUE CA B 401
5AC5SOFTWAREASN B:98 , ASN B:100 , ASP B:130 , ASP B:132 , HIS B:139 , ASP B:184BINDING SITE FOR RESIDUE CA B 402
6AC6SOFTWAREGLU B:11 , GLU B:64 , ASP B:96 , ILE B:97 , ASP B:99 , ASP B:132BINDING SITE FOR RESIDUE CA B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PPE)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Leu A:17 -Pro A:18
2Leu B:17 -Pro B:18
3Asn B:30 -Lys B:31

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PPE)

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CADHERIN_2PS50268 Cadherins domain profile.CADH5_CHICK75-144
 
145-251
 
252-366
367-474
474-582
  4A:35-104
B:35-104
A:105-203
B:105-203
-
-
-
2CADHERIN_1PS00232 Cadherin domain signature.CADH5_CHICK132-142
 
239-249
 
462-472
  4A:92-102
B:92-102
A:199-203
B:199-203
-

(-) Exons   (0, 0)

(no "Exon" information available for 3PPE)

(-) 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:203
 aligned with CADH5_CHICK | Q8AYD0 from UniProtKB/Swiss-Prot  Length:773

    Alignment length:203
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
          CADH5_CHICK    41 DWIWNRMHIREEIDSPLPHHVGKLTSSVGNKNAMYIIEGESANTIFKVQGYDGDIYAFERLDREKKAEYELTAHIIDRRNNRSLEPPSKFIIKVSDINDNAPIFVQKIFNGSVPEMSRLGTSVTKVTAEDADDPTVAGHATVTYQIIKGNEYFTVDDSGVISTARADLDRESQSAYEIIVKAKDALGLTGESSTATVIIRLTD 243
               SCOP domains d3ppea1 A:1-97 automated matches                                                                 d3ppea2 A:98-203 automated matches                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee........eeeee.........eeeeeee......eeee....eeee..........eeeeeeeeee....ee....eeeeeeee.......ee...eeeeeee.......eeee..ee............eeeeeee....eee....eeee...........eeeeeeeeee.........eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------CADHERIN_2  PDB: A:35-104 UniProt: 75-144                             CADHERIN_2  PDB: A:105-203 UniProt: 145-251                                                         PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------CADHERIN_1 ------------------------------------------------------------------------------------------------CADHE PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ppe A   1 DWIWNRMHIREEIDSPLPHHVGKLTSSVGNKNAMYIIEGESANTIFKVQGYDGDIYAFERLDREKKAEYELTAHIIDRRNNRSLEPPSKFIIKVSDINDNAPIFVQKIFNGSVPEMSRLGTSVTKVTAEDADDPTVAGHATVTYQIIKGNEYFTVDDSGVIFTARADLDRESQSAYEIIVKAKDALGLTGESSTATVIIRLTD 203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   

Chain B from PDB  Type:PROTEIN  Length:203
 aligned with CADH5_CHICK | Q8AYD0 from UniProtKB/Swiss-Prot  Length:773

    Alignment length:203
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
          CADH5_CHICK    41 DWIWNRMHIREEIDSPLPHHVGKLTSSVGNKNAMYIIEGESANTIFKVQGYDGDIYAFERLDREKKAEYELTAHIIDRRNNRSLEPPSKFIIKVSDINDNAPIFVQKIFNGSVPEMSRLGTSVTKVTAEDADDPTVAGHATVTYQIIKGNEYFTVDDSGVISTARADLDRESQSAYEIIVKAKDALGLTGESSTATVIIRLTD 243
               SCOP domains d3ppeb1 B:1-97 automated matches                                                                 d3ppeb2 B:98-203 automated matches                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee........eeeee.........eeeeeee......eeee....eeee..........eeeeeeeeee..........eeeeeeee............eeeeeee.......eeee................eeeeeee....eee....eeee...........eeeeeeeeee.........eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------CADHERIN_2  PDB: B:35-104 UniProt: 75-144                             CADHERIN_2  PDB: B:105-203 UniProt: 145-251                                                         PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------CADHERIN_1 ------------------------------------------------------------------------------------------------CADHE PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ppe B   1 DWIWNRMHIREEIDSPLPHHVGKLTSSVGNKNAMYIIEGESANTIFKVQGYDGDIYAFERLDREKKAEYELTAHIIDRRNNRSLEPPSKFIIKVSDINDNAPIFVQKIFNGSVPEMSRLGTSVTKVTAEDADDPTVAGHATVTYQIIKGNEYFTVDDSGVIFTARADLDRESQSAYEIIVKAKDALGLTGESSTATVIIRLTD 203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PPE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3PPE)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CADH5_CHICK | Q8AYD0)
molecular function
    GO:0008013    beta-catenin binding    Interacting selectively and non-covalently with the beta subunit of the catenin complex.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0044325    ion channel binding    Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0019903    protein phosphatase binding    Interacting selectively and non-covalently with any protein phosphatase.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0001955    blood vessel maturation    A developmental process, independent of morphogenetic (shape) change, that is required for a blood vessel to attain its fully functional state.
    GO:0060317    cardiac epithelial to mesenchymal transition    A transition where a cardiac epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0007043    cell-cell junction assembly    The aggregation, arrangement and bonding together of a set of components to form a junction between cells.
    GO:0007156    homophilic cell adhesion via plasma membrane adhesion molecules    The attachment of a plasma membrane adhesion molecule in one cell to an identical molecule in an adjacent cell.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:1903142    positive regulation of establishment of endothelial barrier    Any process that activates or increases the frequency, rate or extent of establishment of endothelial barrier.
    GO:2000114    regulation of establishment of cell polarity    Any process that modulates the frequency, rate or extent of establishment of cell polarity.
    GO:0016337    single organismal cell-cell adhesion    The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism.
    GO:0007179    transforming growth factor beta receptor signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0005912    adherens junction    A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
    GO:0005923    bicellular tight junction    An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0071944    cell periphery    The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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