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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE 10TH PDZ DOMAIN OF MPDZ
 
Authors :  C. Gileadi, C. Phillips, J. Elkins, E. Papagrigoriou, E. Ugochukwu, F. Gorrec, P. Savitsky, C. Umeano, G. Berridge, O. Gileadi, E. Salah, A. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundstrom, D. A. Doyle, Structural Genomics Consortium (Sgc)
Date :  29 Jan 07  (Deposition) - 13 Feb 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Protein, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Gileadi, C. Phillips, J. Elkins, E. Papagrigoriou, E. Ugochukwu, F. Gorrec, P. Savitsky, C. Umeano, G. Berridge, O. Gileadi, E. Salah, A. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundstrom, D. A. Doyle, Structural Genomics Consortium (Sgc)
The Crystal Structure Of The 10Th Pdz Domain Of Mpdz
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MULTIPLE PDZ DOMAIN PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneMPDZ, MUPP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMULTI-PDZ DOMAIN PROTEIN 1

 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  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:1654 , GLN A:1676 , ILE A:1677 , LEU A:1685BINDING SITE FOR RESIDUE NA A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OPG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_056120G1663RMPDZ_HUMANPolymorphism2274648A/BG1663R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_056120G1663RMPDZ_HUMANPolymorphism2274648AG1663R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_056120G1663RMPDZ_HUMANPolymorphism2274648BG1663R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.MPDZ_HUMAN137-224
257-337
377-463
553-634
700-776
1008-1076
1151-1239
1350-1433
1483-1564
1629-1712
 
1725-1807
1862-1948
1987-2070
  2-
-
-
-
-
-
-
-
-
A:1629-1712
B:1629-1712
-
-
-
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.MPDZ_HUMAN137-224
257-337
377-463
553-634
700-776
1008-1076
1151-1239
1350-1433
1483-1564
1629-1712
 
1725-1807
1862-1948
1987-2070
  1-
-
-
-
-
-
-
-
-
A:1629-1712
-
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.MPDZ_HUMAN137-224
257-337
377-463
553-634
700-776
1008-1076
1151-1239
1350-1433
1483-1564
1629-1712
 
1725-1807
1862-1948
1987-2070
  1-
-
-
-
-
-
-
-
-
-
B:1629-1712
-
-
-

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003192171cENSE00001934625chr9:13250328-1325029930MPDZ_HUMAN1-660--
1.2ENST000003192172ENSE00001678863chr9:13247800-13247634167MPDZ_HUMAN6-61560--
1.3ENST000003192173ENSE00001621914chr9:13224582-13224373210MPDZ_HUMAN62-131700--
1.4ENST000003192174ENSE00001664917chr9:13223709-13223570140MPDZ_HUMAN132-178470--
1.5ENST000003192175ENSE00001741916chr9:13222445-13222232214MPDZ_HUMAN178-249720--
1.6ENST000003192176ENSE00001619314chr9:13221499-13221371129MPDZ_HUMAN250-292430--
1.7aENST000003192177aENSE00001641589chr9:13219767-13219558210MPDZ_HUMAN293-362700--
1.8ENST000003192178ENSE00001654162chr9:13217293-13217179115MPDZ_HUMAN363-401390--
1.9ENST000003192179ENSE00001687264chr9:13216861-1321677389MPDZ_HUMAN401-430300--
1.10bENST0000031921710bENSE00001776738chr9:13206098-13205915184MPDZ_HUMAN431-492620--
1.11ENST0000031921711ENSE00001644434chr9:13205106-1320503572MPDZ_HUMAN492-516250--
1.12ENST0000031921712ENSE00001761630chr9:13196229-13196120110MPDZ_HUMAN516-552370--
1.13ENST0000031921713ENSE00001718719chr9:13193312-13193166147MPDZ_HUMAN553-601490--
1.14bENST0000031921714bENSE00001731016chr9:13192294-13192130165MPDZ_HUMAN602-656550--
1.15aENST0000031921715aENSE00001775725chr9:13190298-13190113186MPDZ_HUMAN657-718620--
1.16ENST0000031921716ENSE00001656294chr9:13188992-13188783210MPDZ_HUMAN719-788700--
1.17ENST0000031921717ENSE00001741335chr9:13186385-13186269117MPDZ_HUMAN789-827390--
1.18ENST0000031921718ENSE00001672728chr9:13183584-13183417168MPDZ_HUMAN828-883560--
1.19ENST0000031921719ENSE00001774479chr9:13176416-13176135282MPDZ_HUMAN884-977940--
1.20bENST0000031921720bENSE00001717162chr9:13175874-13175751124MPDZ_HUMAN978-1019420--
1.21ENST0000031921721ENSE00001689243chr9:13168563-13168365199MPDZ_HUMAN1019-1085670--
1.23ENST0000031921723ENSE00001668414chr9:13162794-13162690105MPDZ_HUMAN1085-1120360--
1.24ENST0000031921724ENSE00001677349chr9:13158109-1315801793MPDZ_HUMAN1120-1151320--
1.25ENST0000031921725ENSE00001781999chr9:13150687-13150510178MPDZ_HUMAN1151-1210600--
1.26ENST0000031921726ENSE00001669588chr9:13147657-13147547111MPDZ_HUMAN1211-1247370--
1.27ENST0000031921727ENSE00000689662chr9:13143563-1314346599MPDZ_HUMAN1248-1280330--
1.28ENST0000031921728ENSE00001749448chr9:13140148-13139986163MPDZ_HUMAN1281-1335550--
1.29ENST0000031921729ENSE00001797744chr9:13138152-13137956197MPDZ_HUMAN1335-1400660--
1.30ENST0000031921730ENSE00001674971chr9:13136802-1313671192MPDZ_HUMAN1401-1431310--
1.31aENST0000031921731aENSE00001685780chr9:13136181-1313609191MPDZ_HUMAN1431-1461310--
1.32bENST0000031921732bENSE00001606347chr9:13133903-1313382381MPDZ_HUMAN1462-1488270--
1.33ENST0000031921733ENSE00001640400chr9:13126771-1312667993MPDZ_HUMAN1489-1519310--
1.34ENST0000031921734ENSE00001805659chr9:13126589-1312651575MPDZ_HUMAN1520-1544250--
1.35ENST0000031921735ENSE00001636204chr9:13125389-13125215175MPDZ_HUMAN1545-1603592A:1623-1624
B:1623-1624
2
2
1.36ENST0000031921736ENSE00001624161chr9:13123297-13123152146MPDZ_HUMAN1603-1651492A:1625-1651
B:1625-1651
27
27
1.37ENST0000031921737ENSE00001637999chr9:13122169-1312208684MPDZ_HUMAN1652-1679282A:1652-1679
B:1652-1679
28
28
1.38ENST0000031921738ENSE00001803493chr9:13121931-13121738194MPDZ_HUMAN1680-1744652A:1680-1720
B:1680-1720
41
41
1.39bENST0000031921739bENSE00001659240chr9:13119648-13119501148MPDZ_HUMAN1744-1793500--
1.40bENST0000031921740bENSE00001420090chr9:13115333-1311524787MPDZ_HUMAN1794-1822290--
1.41aENST0000031921741aENSE00001259421chr9:13114020-1311393091MPDZ_HUMAN1823-1853310--
1.42ENST0000031921742ENSE00000689630chr9:13113053-1311301044MPDZ_HUMAN1853-1867150--
1.43ENST0000031921743ENSE00000813304chr9:13112145-13112023123MPDZ_HUMAN1868-1908410--
1.44ENST0000031921744ENSE00000813303chr9:13110739-13110635105MPDZ_HUMAN1909-1943350--
1.45ENST0000031921745ENSE00000689624chr9:13110063-13109951113MPDZ_HUMAN1944-1981380--
1.46ENST0000031921746ENSE00000813301chr9:13109058-13108935124MPDZ_HUMAN1981-2022420--
1.47eENST0000031921747eENSE00001487238chr9:13107110-131057031408MPDZ_HUMAN2023-2070480--

(-) 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:98
 aligned with MPDZ_HUMAN | O75970 from UniProtKB/Swiss-Prot  Length:2070

    Alignment length:121
                                  1609      1619      1629      1639      1649      1659      1669      1679      1689      1699      1709      1719 
          MPDZ_HUMAN   1600 SIRNTSRSSTPAIFASDPATCPIIPGCETTIEISKGRTGLGLSIVGGSDTLLGAIIIHEVYEEGAACKDGRLWAGDQILEVNGIDLRKATHDEAINVLRQTPQRVRLTLYRDEAPYKEEEV 1720
               SCOP domains d2                       opga_ A: Multiple PDZ domain protein                                                             SCOP domains
               CATH domains 2o                       pgA00 A:1623-1720  [code=2.30.42.10, no name defined]                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..-----------------------.eeeeeeee.......eeeee........eeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhh...eeeeeeee......eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------R--------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------PDZ  PDB: A:1629-1712 UniProt: 1629-1712                                            -------- PROSITE
           Transcript 1 (1) 1.35------------------------------------------------Exon 1.37  PDB: A:1652-1679 Exon 1.38  PDB: A:1680-1720 [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.36  PDB: A:1625-1651 UniProt: 1603-1651   --------------------------------------------------------------------- Transcript 1 (2)
                2opg A 1623 SM-----------------------GCETTIEISKGRTGLGLSIVGGSDTLLGAIIIHEVYEEGAACKDGRLWAGDQILEVNGIDLRKATHDEAINVLRQTPQRVRLTLYRDEAPYKSTRL 1720
                             |       -         -     |1629      1639      1649      1659      1669      1679      1689      1699      1709      1719 
                             |                    1625                                                                                               
                          1624                                                                                                                       

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with MPDZ_HUMAN | O75970 from UniProtKB/Swiss-Prot  Length:2070

    Alignment length:121
                                  1609      1619      1629      1639      1649      1659      1669      1679      1689      1699      1709      1719 
          MPDZ_HUMAN   1600 SIRNTSRSSTPAIFASDPATCPIIPGCETTIEISKGRTGLGLSIVGGSDTLLGAIIIHEVYEEGAACKDGRLWAGDQILEVNGIDLRKATHDEAINVLRQTPQRVRLTLYRDEAPYKEEEV 1720
               SCOP domains d2                       opgb_ B: Multiple PDZ domain protein                                                             SCOP domains
               CATH domains 2o                       pgB00 B:1623-1720  [code=2.30.42.10, no name defined]                                            CATH domains
           Pfam domains (1) ---------------------------PDZ-2opgB01 B:1627-1709                                                            ----------- Pfam domains (1)
           Pfam domains (2) ---------------------------PDZ-2opgB02 B:1627-1709                                                            ----------- Pfam domains (2)
         Sec.struct. author ..-----------------------eeeeeeeee.......eeeee........eeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhh...eeeeeeeee.....eeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------R--------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------PDZ  PDB: B:1629-1712 UniProt: 1629-1712                                            -------- PROSITE
           Transcript 1 (1) 1.35------------------------------------------------Exon 1.37  PDB: B:1652-1679 Exon 1.38  PDB: B:1680-1720 [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.36  PDB: B:1625-1651 UniProt: 1603-1651   --------------------------------------------------------------------- Transcript 1 (2)
                2opg B 1623 SM-----------------------GCETTIEISKGRTGLGLSIVGGSDTLLGAIIIHEVYEEGAACKDGRLWAGDQILEVNGIDLRKATHDEAINVLRQTPQRVRLTLYRDEAPYKSTRL 1720
                             |       -         -     |1629      1639      1649      1659      1669      1679      1689      1699      1709      1719 
                          1624                    1625                                                                                               

   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  (1, 2)

Asymmetric Unit
(-)
Clan: PDZ-like (184)
(-)
Family: PDZ (172)
1aPDZ-2opgB01B:1627-1709
1bPDZ-2opgB02B:1627-1709

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MPDZ_HUMAN | O75970)
molecular function
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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: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:0042552    myelination    The process in which myelin sheaths are formed and maintained around neurons. Oligodendrocytes in the brain and spinal cord and Schwann cells in the peripheral nervous system wrap axons with compact layers of their plasma membrane. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0043220    Schmidt-Lanterman incisure    Regions within compact myelin in which the cytoplasmic faces of the enveloping myelin sheath are not tightly juxtaposed, and include cytoplasm from the cell responsible for making the myelin. Schmidt-Lanterman incisures occur in the compact myelin internode, while lateral loops are analogous structures found in the paranodal region adjacent to the nodes of Ranvier.
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0016327    apicolateral plasma membrane    The apical end of the lateral plasma membrane of epithelial cells.
    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:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MPDZ_HUMAN | O759702fcf 2fne 2iwn 2iwo 2iwp 2iwq 2o2t 2qg1

(-) Related Entries Specified in the PDB File

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