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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PTPN4 PDZ DOMAIN COMPLEXED WITH THE C-TERMINUS OF A RABIES VIRUS G PROTEIN
 
Authors :  N. Babault, F. Cordier, M. Lafage, J. Cockburn, A. Haouz, F. A. Rey, M. De H. Buc, M. Lafon, N. Wolff
Date :  10 Jun 10  (Deposition) - 24 Aug 11  (Release) - 30 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.43
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Pdz-Pdz-Binding Site Complex, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Babault, F. Cordier, M. Lafage, J. Cockburn, A. Haouz, C. Prehaud, F. A. Rey, M. Delepierre, H. Buc, M. Lafon, N. Wolff
Peptides Targeting The Pdz Domain Of Ptpn4 Are Efficient Inducers Of Glioblastoma Cell Death.
Structure V. 19 1518 2011
PubMed-ID: 22000519  |  Reference-DOI: 10.1016/J.STR.2011.07.007

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 4
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST15
    Expression System Strain: BL21 (DE3) STAR
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PDZ DOMAIN (UNP RESIDUES 499-604)
    Gene: PTPN4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN-TYROSINE PHOSPHATASE MEG1, PTPASE-MEG1, MEG
 
Molecule 2 - GLYCOPROTEIN G
    Chains: C, D
    Engineered: YES
    Fragment: UNP RESIDUES 512-524
    Organism Scientific: RABIES VIRUS
    Organism Taxid: 11292
    Other Details: CYTO13-ATT PEPTIDE HAS BEEN CHEMICALLY SYNTHETIZED. THE SEQUENCE OCCURS NATURALLY IN RABIES VIRUS G PROTEIN
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D
Biological Unit 3 (1x): A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:61 , HOH A:315 , ASP A:537 , PRO A:549 , GLY A:550 , ASP B:554BINDING SITE FOR RESIDUE GOL A 1
2AC2SOFTWAREHOH A:23 , HOH A:28 , VAL A:547 , ARG A:559 , GLU A:562 , ASP A:580 , ASP B:580 , TRP C:2 , HOH C:53BINDING SITE FOR RESIDUE GOL A 605

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:590 -B:590

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:557 -Pro A:558
2Val B:557 -Pro B:558

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.PTN4_HUMAN517-589
 		  2A:517-589
B:517-589
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.PTN4_HUMAN517-589
 		  1A:517-589
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.PTN4_HUMAN517-589
 		  1-
B:517-589
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.PTN4_HUMAN517-589
 		  2A:517-589
B:517-589

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002637081aENSE00001202414chr2:120517207-120517960754PTN4_HUMAN-00--
1.4bENST000002637084bENSE00002161456chr2:120567413-120567567155PTN4_HUMAN1-46460--
1.5bENST000002637085bENSE00001071386chr2:120620112-120620219108PTN4_HUMAN47-82360--
1.6ENST000002637086ENSE00001071393chr2:120634899-12063494143PTN4_HUMAN83-97150--
1.7bENST000002637087bENSE00001071383chr2:120635040-12063511879PTN4_HUMAN97-123270--
1.9bENST000002637089bENSE00001071380chr2:120639362-12063940645PTN4_HUMAN123-138160--
1.10aENST0000026370810aENSE00001071395chr2:120639673-12063972553PTN4_HUMAN138-156190--
1.11bENST0000026370811bENSE00001071376chr2:120640079-120640199121PTN4_HUMAN156-196410--
1.12ENST0000026370812ENSE00001071384chr2:120643371-12064345888PTN4_HUMAN196-225300--
1.13ENST0000026370813ENSE00001730738chr2:120658294-12065838289PTN4_HUMAN226-255300--
1.14aENST0000026370814aENSE00001694309chr2:120672755-12067281864PTN4_HUMAN255-276220--
1.15ENST0000026370815ENSE00001803769chr2:120677645-120677817173PTN4_HUMAN277-334580--
1.16ENST0000026370816ENSE00001640493chr2:120684174-12068424269PTN4_HUMAN334-357240--
1.17bENST0000026370817bENSE00001645678chr2:120690000-120690125126PTN4_HUMAN357-399430--
1.18aENST0000026370818aENSE00001696851chr2:120692376-120692534159PTN4_HUMAN399-452540--
1.19ENST0000026370819ENSE00001749019chr2:120702657-120702816160PTN4_HUMAN452-505540--
1.20ENST0000026370820ENSE00001771605chr2:120703917-12070400084PTN4_HUMAN506-533282A:513-533
B:512-533		21
22
1.21aENST0000026370821aENSE00001594878chr2:120704094-12070415057PTN4_HUMAN534-552192A:534-552
B:534-552		19
19
1.22ENST0000026370822ENSE00001621051chr2:120709549-120709705157PTN4_HUMAN553-605532A:553-604
B:553-604 (gaps)		52
52
1.23ENST0000026370823ENSE00001731922chr2:120712733-120712899167PTN4_HUMAN605-660560--
1.24ENST0000026370824ENSE00001660931chr2:120714420-12071451091PTN4_HUMAN661-691310--
1.25ENST0000026370825ENSE00001797325chr2:120714592-12071465362PTN4_HUMAN691-711210--
1.26bENST0000026370826bENSE00001751186chr2:120718383-120718529147PTN4_HUMAN712-760490--
1.27ENST0000026370827ENSE00001765275chr2:120720192-120720320129PTN4_HUMAN761-803430--
1.28ENST0000026370828ENSE00001760145chr2:120723073-120723221149PTN4_HUMAN804-853500--
1.29bENST0000026370829bENSE00001771727chr2:120725413-120725548136PTN4_HUMAN853-898460--
1.30cENST0000026370830cENSE00001703057chr2:120734560-1207413946835PTN4_HUMAN899-926280--

(-) 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:92
 aligned with PTN4_HUMAN | P29074 from UniProtKB/Swiss-Prot  Length:926

    Alignment length:92
                                   522       532       542       552       562       572       582       592       602  
           PTN4_HUMAN   513 DNLVLIRMKPDENGRFGFNVKGGYDQKMPVIVSRVAPGTPADLCVPRLNEGDQVVLINGRDIAEHTHDQVVLFIKASCERHSGELMLLVRPN 604
               SCOP domains d3nfka_ A: Tyrosine-protein phosphatase non-receptor type 4, PTPN4                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.........eeeeeehhhheeeeeeee...hhhhhh........eeeee..ee....hhhhhhhhhhhhhhh....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: A:517-589 UniProt: 517-589                                     --------------- PROSITE
               Transcript 1 Exon 1.20            Exon 1.21a         Exon 1.22  PDB: A:553-604 UniProt: 553-605           Transcript 1
                 3nfk A 513 DNLVLIRMKPDENGRFGFNVKGGYDQKMPVIVSRVAPGTPADLCVPRLNEGDQVVLINGRDIAEHTHDQVVLFIKASCERHSGELMLLVRPN 604
                                   522       532       542       552       562       572       582       592       602  


Chain B from PDB  Type:PROTEIN  Length:91
 aligned with PTN4_HUMAN | P29074 from UniProtKB/Swiss-Prot  Length:926

    Alignment length:93
                                   521       531       541       551       561       571       581       591       601   
           PTN4_HUMAN   512 HDNLVLIRMKPDENGRFGFNVKGGYDQKMPVIVSRVAPGTPADLCVPRLNEGDQVVLINGRDIAEHTHDQVVLFIKASCERHSGELMLLVRPN 604
               SCOP domains d3nfkb_ B: Tyrosine-protein phosphatase non-receptor type 4, PTPN4                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.........eeeeeehhhheeeeeeee...hhhhhh........eeeee..ee....hhhhhhhhhhh...--...eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PDZ  PDB: B:517-589 UniProt: 517-589                                     --------------- PROSITE
               Transcript 1 Exon 1.20 [INCOMPLETE]Exon 1.21a         Exon 1.22  PDB: B:553-604 (gaps) UniProt: 553-605    Transcript 1
                 3nfk B 512 HDNLVLIRMKPDENGRFGFNVKGGYDQKMPVIVSRVAPGTPADLCVPRLNEGDQVVLINGRDIAEHTHDQVVLFIKASCE--SGELMLLVRPN 604
                                   521       531       541       551       561       571       581       591  |    601   
                                                                                                         591  |          
                                                                                                            594          


Chain C from PDB  Type:PROTEIN  Length:13
 aligned with GLYCO_RABVE | P03524 from UniProtKB/Swiss-Prot  Length:524

    Alignment length:13
                                   521   
          GLYCO_RABVE   512 SWESHKSGGETRL 524
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author .....ee..eee. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 3nfk C   1 SWESHKSGGETRL  13
                                    10   


Chain D from PDB  Type:PROTEIN  Length:5
 aligned with GLYCO_RABVE | P03524 from UniProtKB/Swiss-Prot  Length:524

    Alignment length:5
          GLYCO_RABVE   520 GETRL 524
               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
                 3nfk D   9 GETRL  13
   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 20)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PTN4_HUMAN | P29074)
molecular function
    GO:0008092    cytoskeletal protein binding    Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004726    non-membrane spanning protein tyrosine phosphatase activity    Catalysis of the reaction: non-membrane spanning protein tyrosine phosphate + H2O = non-membrane spanning protein tyrosine + phosphate.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    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:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
cellular component
    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: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: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.

Chain C,D   (GLYCO_RABVE | P03524)
cellular component
    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:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PTN4_HUMAN | P29074: 2cs5 2i75 2vph 3nfl 5eyz 5ez0

(-) Related Entries Specified in the PDB File

2cs5 SOLUTION STRUCTURE OF PTPN4-PDZ
2vph CRYSTAL STRUCTURE OF PTPN4-PDZ
3nfl