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(-) Description

Title :  CRYSTAL STRUCTURE OF ERBIN PDZ
 
Authors :  B. A. Appleton, Y. Zhang, P. Wu, J. P. Yin, W. Hunziker, N. J. Skelton, S. S. Sidhu, C. Wiesmann
Date :  22 May 06  (Deposition) - 13 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pdz Domain, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. A. Appleton, Y. Zhang, P. Wu, J. P. Yin, W. Hunziker, N. J. Skelton, S. S. Sidhu, C. Wiesmann
Comparative Structural Analysis Of The Erbin Pdz Domain And The First Pdz Domain Of Zo-1. Insights Into Determinants Of Pdz Domain Specificity.
J. Biol. Chem. V. 281 22312 2006
PubMed-ID: 16737969  |  Reference-DOI: 10.1074/JBC.M602901200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LAP2 PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET22D
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentPDZ DOMAIN
    GeneERBIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymERBB2-INTERACTING PROTEIN, ERBIN, DENSIN-180-LIKE PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2H3L)

(-) Sites  (0, 0)

(no "Site" information available for 2H3L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2H3L)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:1329 -Pro A:1330
2Asp B:1329 -Pro B:1330

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H3L)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.ERBIN_HUMAN1321-1410
 
  2A:1321-1410
B:1321-1410
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.ERBIN_HUMAN1321-1410
 
  1A:1321-1410
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.ERBIN_HUMAN1321-1410
 
  1-
B:1321-1410

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002840371aENSE00001850711chr5:65222303-65222634332ERBIN_HUMAN-00--
1.3bENST000002840373bENSE00001147720chr5:65284463-6528451048ERBIN_HUMAN-00--
1.4ENST000002840374ENSE00000912221chr5:65288538-65288735198ERBIN_HUMAN1-63630--
1.5ENST000002840375ENSE00000912222chr5:65290575-65290692118ERBIN_HUMAN64-103400--
1.6ENST000002840376ENSE00000912223chr5:65307877-6530795579ERBIN_HUMAN103-129270--
1.7ENST000002840377ENSE00000837126chr5:65309377-6530946690ERBIN_HUMAN129-159310--
1.8ENST000002840378ENSE00000837127chr5:65310497-6531055357ERBIN_HUMAN159-178200--
1.9ENST000002840379ENSE00000912224chr5:65317150-6531721364ERBIN_HUMAN178-199220--
1.10bENST0000028403710bENSE00000912225chr5:65319118-6531919275ERBIN_HUMAN200-224250--
1.11bENST0000028403711bENSE00000912226chr5:65320134-65320278145ERBIN_HUMAN225-273490--
1.12bENST0000028403712bENSE00000912227chr5:65321308-6532138073ERBIN_HUMAN273-297250--
1.13ENST0000028403713ENSE00000912228chr5:65321676-65321805130ERBIN_HUMAN297-340440--
1.14ENST0000028403714ENSE00000912229chr5:65322130-65322245116ERBIN_HUMAN341-379390--
1.15ENST0000028403715ENSE00000912230chr5:65324102-6532417170ERBIN_HUMAN379-402240--
1.16ENST0000028403716ENSE00000912231chr5:65334211-65334310100ERBIN_HUMAN403-436340--
1.17ENST0000028403717ENSE00000912232chr5:65338905-65339026122ERBIN_HUMAN436-476410--
1.18bENST0000028403718bENSE00000912233chr5:65339965-65340138174ERBIN_HUMAN477-534580--
1.19ENST0000028403719ENSE00000912234chr5:65342181-65342366186ERBIN_HUMAN535-596620--
1.20ENST0000028403720ENSE00000749858chr5:65344495-65344609115ERBIN_HUMAN597-635390--
1.21ENST0000028403721ENSE00000912235chr5:65346611-65346794184ERBIN_HUMAN635-696620--
1.22aENST0000028403722aENSE00000837128chr5:65349234-653507791546ERBIN_HUMAN696-12115160--
1.25aENST0000028403725aENSE00001082465chr5:65367997-65368119123ERBIN_HUMAN1212-1252410--
1.26bENST0000028403726bENSE00002155220chr5:65370852-65371058207ERBIN_HUMAN1253-1321692A:1310-1321
B:1314-1321
12
8
1.27bENST0000028403727bENSE00000837130chr5:65372144-6537223693ERBIN_HUMAN1322-1352312A:1322-1352
B:1322-1352
31
31
1.27eENST0000028403727eENSE00000837131chr5:65372703-6537277775ERBIN_HUMAN1353-1377252A:1353-1377
B:1353-1377
25
25
1.28jENST0000028403728jENSE00001896859chr5:65374251-653783774127ERBIN_HUMAN1378-1412352A:1378-1412
B:1378-1411
35
34

(-) Sequences/Alignments

Asymmetric 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:103
 aligned with ERBIN_HUMAN | Q96RT1 from UniProtKB/Swiss-Prot  Length:1412

    Alignment length:103
                                  1319      1329      1339      1349      1359      1369      1379      1389      1399      1409   
         ERBIN_HUMAN   1310 SPRQGHELAKQEIRVRVEKDPELGFSISGGVGGRGNPFRPDDDGIFVTRVQPEGPASKLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQNTVELIIVREVSS 1412
               SCOP domains d2h3la_ A: Erbin                                                                                        SCOP domains
               CATH domains 2h3lA00 A:1310-1412  [code=2.30.42.10, no name defined]                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeee......eeeee...............eeeeee..............eeeee..ee....hhhhhhhhhhhh..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------PDZ  PDB: A:1321-1410 UniProt: 1321-1410                                                  -- PROSITE
               Transcript 1 Exon 1.26b  Exon 1.27b  PDB: A:1322-1352   Exon 1.27e               Exon 1.28j  PDB: A:1378-1412        Transcript 1
                2h3l A 1310 GSHMGHELAKQEIRVRVEKDPELGFSISGGVGGRGNPFRPDDDGIFVTRVQPEGPASKLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQNTVELIIVREVSS 1412
                                  1319      1329      1339      1349      1359      1369      1379      1389      1399      1409   

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with ERBIN_HUMAN | Q96RT1 from UniProtKB/Swiss-Prot  Length:1412

    Alignment length:98
                                  1323      1333      1343      1353      1363      1373      1383      1393      1403        
         ERBIN_HUMAN   1314 GHELAKQEIRVRVEKDPELGFSISGGVGGRGNPFRPDDDGIFVTRVQPEGPASKLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQNTVELIIVREVS 1411
               SCOP domains d2h3lb_ B: Erbin                                                                                   SCOP domains
               CATH domains 2h3lB00 B:1314-1411  [code=2.30.42.10, no name defined]                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee......eeeee...............eeeeee..............eeeee..ee....hhhhhhhhhhhh..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------PDZ  PDB: B:1321-1410 UniProt: 1321-1410                                                  - PROSITE
               Transcript 1 1.26b   Exon 1.27b  PDB: B:1322-1352   Exon 1.27e               Exon 1.28j  PDB: B:1378-1411       Transcript 1
                2h3l B 1314 GHELAKQEIRVRVEKDPELGFSISGGVGGRGNPFRPDDDGIFVTRVQPEGPASKLLQPGDKIIQANGYSFINIEHGQAVSLLKTFQNTVELIIVREVS 1411
                                  1323      1333      1343      1353      1363      1373      1383      1393      1403        

   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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H3L)

(-) Gene Ontology  (33, 33)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ERBIN_HUMAN | Q96RT1)
molecular function
    GO:0005176    ErbB-2 class receptor binding    Interacting selectively and non-covalently with the protein-tyrosine kinase receptor Neu/ErbB-2/HER2.
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    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).
    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.
    GO:0005200    structural constituent of cytoskeleton    The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
biological process
    GO:0038128    ERBB2 signaling pathway    A series of molecular signals initiated by binding of a ligand to a member of the ERBB family of receptors on the surface of a cell, where the signal is transmitted by ERBB2. The pathway ends with regulation of a downstream cellular process, e.g. transcription. ERBB2 receptors are themselves unable to bind to ligands, but act as a signal-amplifying tyrosine kinase within a heterodimeric pair.
    GO:0045175    basal protein localization    Any process in which a protein is transported to, or maintained in, basal regions of the 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:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0016049    cell growth    The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
    GO:0071356    cellular response to tumor necrosis factor    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 tumor necrosis factor stimulus.
    GO:0007173    epidermal growth factor receptor signaling pathway    A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0045197    establishment or maintenance of epithelial cell apical/basal polarity    Any cellular process that results in the specification, formation or maintenance of the apicobasal polarity of an epithelial cell.
    GO:0007229    integrin-mediated signaling pathway    A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0045104    intermediate filament cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising intermediate filaments and their associated proteins.
    GO:0032088    negative regulation of NF-kappaB transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB.
    GO:0071638    negative regulation of monocyte chemotactic protein-1 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of production of monocyte chemotactic protein-1.
    GO:0070433    negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway    Any process that stops, prevents, or reduces the frequency, rate, or extent of the nucleotide-binding oligomerization domain containing 2 (NOD2) pathway.
    GO:0006605    protein targeting    The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0032495    response to muramyl dipeptide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a muramyl dipeptide stimulus. Muramyl dipeptide is derived from peptidoglycan.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0009925    basal plasma membrane    The region of the plasma membrane located at the basal end of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    GO:0005604    basement membrane    A thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers.
    GO:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030056    hemidesmosome    A cell-substrate junction (attachment structure) found in epithelial cells that links intermediate filaments to extracellular matrices via transmembrane complexes. In vertebrates, hemidesmosomes mediate contact between the basal side of epithelial cells and the basal lamina. In C. elegans, hemidesmosomes connect epithelial cells to distinct extracellular matrices on both the apical and basal cell surfaces.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        ERBIN_HUMAN | Q96RT11mfg 1mfl 1n7t 2qbw 3ch8

(-) Related Entries Specified in the PDB File

2h2b 2h2c 2h3m