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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PDZ TANDEM OF HUMAN SYNTENIN IN COMPLEX WITH TNEYKV PEPTIDE
 
Authors :  J. Grembecka, T. Cierpicki, Y. Devedjiev, D. R. Cooper, U. Derewenda, Z. S. Derewenda
Date :  23 Apr 04  (Deposition) - 14 Jun 05  (Release) - 30 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,S,T
Keywords :  Cell Adhesion, Adhesion/Complex, Pdz Domain, Scaffolding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Grembecka, T. Cierpicki, Y. Devedjiev, U. Derewenda, B. S. Kang, J. H. Bushweller, Z. S. Derewenda
The Binding Of The Pdz Tandem Of Syntenin To Target Proteins.
Biochemistry V. 45 3674 2006
PubMed-ID: 16533050  |  Reference-DOI: 10.1021/BI052225Y

(-) Compounds

Molecule 1 - SYNTENIN 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGST-PARALLEL1
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: PDZ TANDEM, RESIDUES 108-273
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: GENE, SDCBP OR MDA9 OR SYCL
    Synonym: SYNDECAN BINDING PROTEIN 1, MELANOMA DIFFERENTIATION ASSOCIATED PROTEIN-9, MDA-9, SCAFFOLD PROTEIN PBP1, PRO-TGF-ALPHA CYTOPLASMIC DOMAIN- INTERACTING PROTEIN 18, TACIP18
 
Molecule 2 - TNEYKV PEPTIDE
    Chains: S, T
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABST

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1BEZ1Ligand/IonBENZOIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:120 , GLY A:126 , ASN A:144 , SER A:145 , PRO A:146 , HIS A:202 , SER A:226 , ARG A:229 , ASN A:230BINDING SITE FOR RESIDUE BEZ A1274

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V1T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V1T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V1T)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.SDCB1_HUMAN114-193
 
198-273
 		  4A:114-193
B:114-193
A:198-273
B:198-272

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002601301bENSE00001423873chr8:59465728-59465862135SDCB1_HUMAN-00--
1.3cENST000002601303cENSE00002198946chr8:59477578-5947764366SDCB1_HUMAN1-17170--
1.4bENST000002601304bENSE00000928399chr8:59483446-5948352479SDCB1_HUMAN18-44270--
1.5cENST000002601305cENSE00000928400chr8:59484764-59484873110SDCB1_HUMAN44-80370--
1.6aENST000002601306aENSE00000928401chr8:59488459-59488620162SDCB1_HUMAN81-134542A:110-134
B:111-134 (gaps)		25
50
1.7cENST000002601307cENSE00000928402chr8:59490592-59490767176SDCB1_HUMAN135-193592A:135-193
B:135-193		59
59
1.8aENST000002601308aENSE00000928403chr8:59492182-59492353172SDCB1_HUMAN193-250582A:193-250
B:193-250		58
58
1.9ENST000002601309ENSE00000928404chr8:59493076-5949316792SDCB1_HUMAN251-281312A:251-273
B:251-272		23
22
1.10hENST0000026013010hENSE00002117339chr8:59494245-594954191175SDCB1_HUMAN281-298180--

(-) 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:164
 aligned with SDCB1_HUMAN | O00560 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:164
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269    
          SDCB1_HUMAN   110 QGIREVILCKDQDGKIGLRLKSIDNGIFVQLVQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKITMTIRDRPFERTITMHKDSTGHVGFIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPAF 273
               SCOP domains d1v1ta1 A:110-194 Syntenin 1                                                         d1v1ta2 A:195-273 Syntenin 1                                                    SCOP domains
               CATH domains 1v1tA01 A:110-194  [code=2.30.42.10, no name defined]                                1v1tA02 A:195-273  [code=2.30.42.10, no name defined]                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee........eeeeee..eeeeeee...hhhhhh......eeeee..ee....hhhhhhhhhhhh...eeeeeee.....eeeeee........eeee..eeeee...hhhhhh.....eeeeee..ee....hhhhhhhhhhhh..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: A:114-193 UniProt: 114-193                                            ----PDZ  PDB: A:198-273 UniProt: 198-273                                         PROSITE
           Transcript 1 (1) Exon 1.6a  PDB: A:110-134Exon 1.7c  PDB: A:135-193 UniProt: 135-193                 ---------------------------------------------------------Exon 1.9  PDB: A:251-27 Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------Exon 1.8a  PDB: A:193-250 UniProt: 193-250                ----------------------- Transcript 1 (2)
                 1v1t A 110 MDPREVILCKDQDGKIGLRLKSIDNGIFVQLVQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKITMTIRDRPFERTITMHKDSTGHVGFIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPAF 273
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269    


Chain B from PDB  Type:PROTEIN  Length:162
 aligned with SDCB1_HUMAN | O00560 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:188
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264        
          SDCB1_HUMAN    85 RPSSINYMVAPVTGNDVGIRRAEIKQGIREVILCKDQDGKIGLRLKSIDNGIFVQLVQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKITMTIRDRPFERTITMHKDSTGHVGFIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPA 272
               SCOP domains d1                          v1tb1 B:111-194 Syntenin 1                                                        d1v1tb2 B:195-272 Syntenin 1                                                   SCOP domains
               CATH domains 1v                          1tB01 B:111-194  [code=2.30.42.10, no name defined]                               1v1tB02 B:195-272  [code=2.30.42.10, no name defined]                          CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------PDZ-1v1tB01 B:198-270                                                    -- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------PDZ-1v1tB02 B:198-270                                                    -- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------PDZ-1v1tB03 B:198-270                                                    -- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------PDZ-1v1tB04 B:198-270                                                    -- Pfam domains (4)
         Sec.struct. author ..--------------------------eeeeee........eeeeee..eeeeeee...hhhhhh......eeeee..ee....hhhhhhhhhhhh...eeeeeee.....eeeeee........eeee..eeeee...hhhhhh.....eeeeee..ee....hhhhhhhhhhh...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------PDZ  PDB: B:114-193 UniProt: 114-193                                            ----PDZ  PDB: B:198-272 UniProt: 198-273                                        PROSITE
           Transcript 1 (1) Exon 1.6a  PDB: B:111-134 (gaps) UniProt: 81-134  Exon 1.7c  PDB: B:135-193 UniProt: 135-193                 ---------------------------------------------------------Exon 1.9 [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------Exon 1.8a  PDB: B:193-250 UniProt: 193-250                ---------------------- Transcript 1 (2)
                 1v1t B 111 DP--------------------------REVILCKDQDGKIGLRLKSIDNGIFVQLVQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKITMTIRDRPFERTITMHKDSTGHVGFIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPA 272
                             |       -         -       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264        
                           112                        113                                                                                                                                                               


Chain S from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..eee Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 1v1t S   2 NEYKV   6


Chain T from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..eee Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 1v1t T   2 NEYKV   6
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: PDZ-like (184)
(-)
Family: PDZ (172)
(-)
Homo sapiens (Human) (96)
1aPDZ-1v1tB01B:198-270
1bPDZ-1v1tB02B:198-270
1cPDZ-1v1tB03B:198-270
1dPDZ-1v1tB04B:198-270

(-) Gene Ontology  (53, 53)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SDCB1_HUMAN | O00560)
molecular function
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    GO:0008093    cytoskeletal adaptor activity    The binding activity of a molecule that brings together a cytoskeletal protein and one or more other molecules, permitting them to function in a coordinated way.
    GO:0046875    ephrin receptor binding    Interacting selectively and non-covalently with an ephrin receptor.
    GO:0005109    frizzled binding    Interacting selectively and non-covalently with the frizzled (fz) receptor.
    GO:0019838    growth factor binding    Interacting selectively and non-covalently with any growth factor, proteins or polypeptides that stimulate a cell or organism to grow or proliferate.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005137    interleukin-5 receptor binding    Interacting selectively and non-covalently with the interleukin-5 receptor.
    GO:0042043    neurexin family protein binding    Interacting selectively and non-covalently with neurexins, synaptic cell surface proteins related to latrotoxin receptor, laminin and agrin. Neurexins act as cell recognition molecules at nerve terminals.
    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:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) 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).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0045545    syndecan binding    Interacting selectively and non-covalently with syndecan, an integral membrane proteoglycan (250-300 kDa) associated largely with epithelial cells.
biological process
    GO:0007265    Ras protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
    GO:0030036    actin 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 actin filaments and their associated proteins.
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0048013    ephrin receptor signaling pathway    The series of molecular signals generated as a consequence of an ephrin receptor binding to an ephrin.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0032435    negative regulation of proteasomal ubiquitin-dependent protein catabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0002091    negative regulation of receptor internalization    Any process that stops, prevents, or reduces the frequency, rate or extent of receptor internalization.
    GO:0046330    positive regulation of JNK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the JNK cascade.
    GO:0030307    positive regulation of cell growth    Any process that activates or increases the frequency, rate, extent or direction of cell growth.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0010718    positive regulation of epithelial to mesenchymal transition    Any process that increases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition is where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
    GO:1903543    positive regulation of exosomal secretion    Any process that activates or increases the frequency, rate or extent of exosomal secretion.
    GO:1903553    positive regulation of extracellular exosome assembly    Any process that activates or increases the frequency, rate or extent of extracellular vesicular exosome assembly.
    GO:0010862    positive regulation of pathway-restricted SMAD protein phosphorylation    Any process that increases the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
    GO:0042327    positive regulation of phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
    GO:0030511    positive regulation of transforming growth factor beta receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of TGF-beta receptor signaling pathway activity.
    GO:0006612    protein targeting to membrane    The process of directing proteins towards a membrane, usually using signals contained within the protein.
    GO:0007346    regulation of mitotic cell cycle    Any process that modulates the rate or extent of progress through the mitotic cell cycle.
    GO:0006930    substrate-dependent cell migration, cell extension    The formation of a cell surface protrusion, such as a lamellipodium or filopodium, at the leading edge of a migrating cell.
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:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    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:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:1903561    extracellular vesicle    Any vesicle that is part of the extracellular region.
    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:0005895    interleukin-5 receptor complex    A protein complex that binds interleukin-3; comprises an alpha and a beta subunit. The alpha chain is specific to the interleukin-5 receptor, whereas the beta chain is shared with the receptors for granulocyte-macrophage colony-stimulating factor and interleukin-3.
    GO:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    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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  1v1t
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 Related Entries

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

UniProtKB/Swiss-Prot
        SDCB1_HUMAN | O00560: 1n99 1nte 1obx 1oby 1obz 1r6j 1w9e 1w9o 1w9q 1ybo 4z33

(-) Related Entries Specified in the PDB File

1n99 CRYSTAL STRUCTURE OF THE PDZ TANDEM OF HUMAN SYNTENIN
1nte CRYSTAL STRUCTURE ANALYSIS OF THE SECOND PDZ DOMAIN OFSYNTENIN
1obx CRYSTAL STRUCTURE OF THE COMPLEX OF PDZ2 OF SYNTENIN WITH AN INTERLEUKIN 5 RECEPTOR ALPHA PEPTIDE.
1oby CRYSTAL STRUCTURE OF THE COMPLEX OF PDZ2 OF SYNTENIN WITH AN INTERLEUKIN 5 RECEPTOR ALPHA PEPTIDE.
1obz CRYSTAL STRUCTURE OF THE COMPLEX OF THE PDZ TANDEM OF SYNTENIN WITH AN INTERLEUKIN 5 RECEPTOR ALPHA PEPTIDE.