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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF HUMAN E-CADHERIN (1-213)
 
Authors :  E. Parisini, J. -H. Wang
Date :  09 Dec 06  (Deposition) - 09 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ig-Like Domains, Calcium-Binding Protein, Cell Adhesion, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Parisini, J. M. G. Higgins, J. -H. Liu, M. B. Brenner, J. -H. Wang
The Crystal Structure Of Human E-Cadherin Domains 1 And 2, And Comparison With Other Cadherins In The Context Of Adhesion Mechanism
J. Mol. Biol. V. 373 401 2007
PubMed-ID: 17850815  |  Reference-DOI: 10.1016/J.JMB.2007.08.011
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EPITHELIAL-CADHERIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAINS 1 AND 2, RESIDUES 155-317
    Gene: CDH1, CDHE, UVO
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1CA5Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:102 , ASN A:104 , ASP A:134 , ASP A:136 , ASN A:143 , ASP A:195BINDING SITE FOR RESIDUE CA A 401
2AC2SOFTWAREGLU A:11 , GLU A:69 , ASP A:100 , GLN A:101 , ASP A:103 , ASP A:136BINDING SITE FOR RESIDUE CA A 402
3AC3SOFTWAREGLU A:11 , ASP A:67 , GLU A:69 , ASP A:103 , HOH A:428 , HOH A:479BINDING SITE FOR RESIDUE CA A 403
4AC4SOFTWAREGLN A:110 , GLU A:119 , ASP A:180 , CA A:405 , HOH A:624 , HOH A:639BINDING SITE FOR RESIDUE CA A 404
5AC5SOFTWAREGLU A:119 , ARG A:181 , GLU A:182 , ASP A:213 , CA A:404 , HOH A:546 , HOH A:624BINDING SITE FOR RESIDUE CA A 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O72)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Gly A:15 -Pro A:16
2Phe A:17 -Pro A:18
3Pro A:46 -Pro A:47
4Asp A:154 -Pro A:155
5Leu A:157 -Pro A:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (7, 7)

Asymmetric Unit (7, 7)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_001307T193PCADH1_HUMANUnclassified  ---AT39P
2UniProtVAR_008712D244GCADH1_HUMANDisease (HDGC)  ---AD90G
3UniProtVAR_013970S270ACADH1_HUMANPolymorphism587776399AS116A
4UniProtVAR_033026M282ICADH1_HUMANUnclassified200932258AM128I
5UniProtVAR_001309N315SCADH1_HUMANUnclassified  ---AN161S
6UniProtVAR_001310E336DCADH1_HUMANPolymorphism267606712AE182D
7UniProtVAR_013971T340ACADH1_HUMANPolymorphism116093741AT186A
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (7, 14)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_001307T193PCADH1_HUMANUnclassified  ---AT39P
2UniProtVAR_008712D244GCADH1_HUMANDisease (HDGC)  ---AD90G
3UniProtVAR_013970S270ACADH1_HUMANPolymorphism587776399AS116A
4UniProtVAR_033026M282ICADH1_HUMANUnclassified200932258AM128I
5UniProtVAR_001309N315SCADH1_HUMANUnclassified  ---AN161S
6UniProtVAR_001310E336DCADH1_HUMANPolymorphism267606712AE182D
7UniProtVAR_013971T340ACADH1_HUMANPolymorphism116093741AT186A
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CADHERIN_2PS50268 Cadherins domain profile.CADH1_HUMAN180-262
263-375
376-486
487-595
594-702		  2A:26-108
A:109-213
-
-
-
2CADHERIN_1PS00232 Cadherin domain signature.CADH1_HUMAN250-260
363-373
583-593		  2A:96-106
A:209-213
-
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CADHERIN_2PS50268 Cadherins domain profile.CADH1_HUMAN180-262
263-375
376-486
487-595
594-702		  4A:26-108
A:109-213
-
-
-
2CADHERIN_1PS00232 Cadherin domain signature.CADH1_HUMAN250-260
363-373
583-593		  4A:96-106
A:209-213
-

(-) Exons   (5, 5)

Asymmetric Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002617691aENSE00001859184chr16:68771128-68771366239CADH1_HUMAN1-16160--
1.2ENST000002617692ENSE00000844392chr16:68772200-68772314115CADH1_HUMAN17-55390--
1.3bENST000002617693bENSE00000946584chr16:68835573-68835796224CADH1_HUMAN55-129750--
1.4bENST000002617694bENSE00000946585chr16:68842327-68842470144CADH1_HUMAN130-177481A:1-2323
1.5ENST000002617695ENSE00000946586chr16:68842596-68842751156CADH1_HUMAN178-229521A:24-7552
1.6ENST000002617696ENSE00000946587chr16:68844100-68844244145CADH1_HUMAN230-278491A:76-12449
1.7ENST000002617697ENSE00000946588chr16:68845587-68845762176CADH1_HUMAN278-336591A:124-18259
1.8ENST000002617698ENSE00000946589chr16:68846038-68846166129CADH1_HUMAN337-379431A:183-21331
1.9ENST000002617699ENSE00000946590chr16:68847216-68847398183CADH1_HUMAN380-440610--
1.11ENST0000026176911ENSE00002191003chr16:68849418-68849662245CADH1_HUMAN441-522820--
1.12ENST0000026176912ENSE00001694152chr16:68853183-68853328146CADH1_HUMAN522-571500--
1.13ENST0000026176913ENSE00001754940chr16:68855904-68856128225CADH1_HUMAN571-646760--
1.14ENST0000026176914ENSE00001721514chr16:68857302-68857529228CADH1_HUMAN646-722770--
1.15ENST0000026176915ENSE00001736533chr16:68862077-68862207131CADH1_HUMAN722-765440--
1.16ENST0000026176916ENSE00001782571chr16:68863557-68863700144CADH1_HUMAN766-813480--
1.17bENST0000026176917bENSE00001930498chr16:68867193-688694372245CADH1_HUMAN814-882690--

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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:213
 aligned with CADH1_HUMAN | P12830 from UniProtKB/Swiss-Prot  Length:882

    Alignment length:213
                                   164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364   
          CADH1_HUMAN   155 DWVIPPISCPENEKGPFPKNLVQIKSNKDKEGKVFYSITGQGADTPPVGVFIIERETGWLKVTEPLDRERIATYTLFSHAVSSNGNAVEDPMEILITVTDQNDNKPEFTQEVFKGSVMEGALPGTSVMEVTATDADDDVNTYNAAIAYTILSQDPELPDKNMFTINRNTGVISVVTTGLDRESFPTYTLVVQAADLQGEGLSTTATAVITVTD 367
               SCOP domains d2o72a1 A:1-101 E-cadherin (epithelial)                                                              d2o72a2 A:102-213 E-cadherin (epithelial)                                                                        SCOP domains
               CATH domains --2o72A01 A:3-101 Cadherins                                                                          2o72A02 A:102-213 Cadherins                                                                                      CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------Cadherin-2o72A01 A:113-212                                                                          - Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------Cadherin-2o72A02 A:113-212                                                                          - Pfam domains (2)
         Sec.struct. author ......eeee........eeeee..hhhhhh..eeeeee...........eee.....eeee..........eeeeeeeeee.........eeeeeeee.......ee...eeeeeee.......eeee..ee.............eeeeeeee........eee.....eeee...........eeeeeeeee.......eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------P--------------------------------------------------G-------------------------A-----------I--------------------------------S--------------------D---A--------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------CADHERIN_2  PDB: A:26-108 UniProt: 180-262                                         CADHERIN_2  PDB: A:109-213 UniProt: 263-375                                                               PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------CADHERIN_1 ------------------------------------------------------------------------------------------------------CADHE PROSITE (2)
           Transcript 1 (1) Exon 1.4b  PDB: A:1-23 Exon 1.5  PDB: A:24-75 UniProt: 178-229             Exon 1.6  PDB: A:76-124 UniProt: 230-278         ----------------------------------------------------------Exon 1.8  PDB: A:183-213        Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: A:124-182 UniProt: 278-336                  ------------------------------- Transcript 1 (2)
                 2o72 A   1 DWVIPPISSPENEKGPFPKNLVQIKSNKDKEGKVFYSITGQGADTPPVGVFIIERETGWLKVTEPLDRERIATYTLFSHAVSSNGNAVEDPMEILITVTDQNDNKPEFTQEVFKGSVMEGALPGTSVMEVTATDADDDVNTYNAAIAYTILSQDPELPDKNMFTINRNTGVISVVTTGLDRESFPTYTLVVQAADLQGEGLSTTATAVITVTD 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: E-set (290)

(-) Gene Ontology  (49, 49)

Asymmetric Unit(hide GO term definitions)
Chain A   (CADH1_HUMAN | P12830)
molecular function
    GO:0032794    GTPase activating protein binding    Interacting selectively and non-covalently with a GTPase activating protein.
    GO:0030506    ankyrin binding    Interacting selectively and non-covalently with ankyrin, a 200 kDa cytoskeletal protein that attaches other cytoskeletal proteins to integral membrane proteins.
    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:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    GO:0045295    gamma-catenin binding    Interacting selectively and non-covalently with the gamma subunit of the catenin complex.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0034332    adherens junction organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an adherens junction. An adherens junction is a cell junction at which the cytoplasmic face of the plasma membrane is attached to actin filaments.
    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:0071681    cellular response to indole-3-methanol    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an indole-3-methanol stimulus.
    GO:0071285    cellular response to lithium ion    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lithium (Li+) ion stimulus.
    GO:0090002    establishment of protein localization to plasma membrane    The directed movement of a protein to a specific location in the plasma membrane.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    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:0022408    negative regulation of cell-cell adhesion    Any process that stops, prevents or reduces the rate or extent of cell adhesion to another cell.
    GO:0031175    neuron projection development    The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0021983    pituitary gland development    The progression of the pituitary gland over time from its initial formation until its mature state. The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands.
    GO:0042993    positive regulation of transcription factor import into nucleus    Any process that activates or increases the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0072659    protein localization to plasma membrane    A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0010033    response to organic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
    GO:0009636    response to toxic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
    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:0007416    synapse assembly    The aggregation, arrangement and bonding together of a set of components to form a synapse. This process ends when the synapse is mature (functional).
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0016235    aggresome    An inclusion body formed by dynein-dependent retrograde transport of an aggregated protein on microtubules.
    GO:0043296    apical junction complex    A functional unit located near the cell apex at the points of contact between epithelial cells, which in vertebrates is composed of the tight junction, the zonula adherens, and desmosomes and in some invertebrates, such as Drosophila, is composed of the subapical complex (SAC), the zonula adherens and the septate junction. Functions in the regulation of cell polarity, tissue integrity and intercellular adhesion and permeability.
    GO:0016342    catenin complex    Complex of peripheral cytoplasmic proteins (alpha-, beta- and gamma-catenin) that interact with the cytoplasmic region of uvomorulin/E-cadherin to connect it to the actin cytoskeleton.
    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:0005913    cell-cell adherens junction    An adherens junction which connects a cell to another cell.
    GO:0030864    cortical actin cytoskeleton    The portion of the actin cytoskeleton, comprising filamentous actin and associated proteins, that lies just beneath the plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016600    flotillin complex    A protein complex that contains flotillin-1 and flotillin-2, and may contain associated proteins. Flotillins associate into membrane microdomains resembling caveolae.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    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:0030027    lamellipodium    A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
    GO:0016328    lateral plasma membrane    The portion of the plasma membrane at the lateral side of the cell. In epithelial cells, lateral plasma membranes are on the sides of cells which lie at the interface of adjacent cells.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

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  2o72
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(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CADH1_HUMAN | P12830: 1o6s 2omt 2omu 2omv 2omx 2omy 2omz 3ff7 3ff8 3l6x 3l6y 4zt1 4zte

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2O72)