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(-) Description

Title :  SOLUTION STRUCTURES OF THE 6TH FN3 DOMAIN OF HUMAN RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE F
 
Authors :  M. Sato, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  25 Apr 06  (Deposition) - 25 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Lar Protein, Leukocyte Antigen Related, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Sato, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structures Of The 6Th Fn3 Domain Of Human Receptor-Type Tyrosine-Protein Phosphatase F
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE F
    ChainsA
    EC Number3.1.3.48
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP050719-01
    Expression System Vector TypePLASMID
    FragmentFIBRONECTIN TYPE III DOMAIN
    GenePTPRF, LAR
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymLAR PROTEIN, LEUKOCYTE ANTIGEN RELATED

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2DN7)

(-) Sites  (0, 0)

(no "Site" information available for 2DN7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DN7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DN7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DN7)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FN3PS50853 Fibronectin type-III domain profile.PTPRF_HUMAN321-411
416-510
514-604
609-706
711-819
820-914
918-1010
1014-1098
  2-
-
-
-
-
A:9-101
A:104-107
-

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3aENST000003599473aENSE00001268253chr1:43996547-43996761215PTPRF_HUMAN-00--
1.4ENST000003599474ENSE00001369939chr1:44003869-4400394880PTPRF_HUMAN-00--
1.5bENST000003599475bENSE00002190863chr1:44010702-44010837136PTPRF_HUMAN1-31310--
1.6cENST000003599476cENSE00001612970chr1:44019163-44019308146PTPRF_HUMAN31-79490--
1.7ENST000003599477ENSE00001771120chr1:44019471-44019612142PTPRF_HUMAN80-127480--
1.8ENST000003599478ENSE00001723929chr1:44035261-44035449189PTPRF_HUMAN127-190640--
1.10aENST0000035994710aENSE00001705341chr1:44044481-44044591111PTPRF_HUMAN190-227380--
1.13ENST0000035994713ENSE00001706696chr1:44054402-44054671270PTPRF_HUMAN227-317910--
1.14bENST0000035994714bENSE00001714914chr1:44056643-44057224582PTPRF_HUMAN317-5111950--
1.15ENST0000035994715ENSE00001636757chr1:44057483-44057619137PTPRF_HUMAN511-556460--
1.16ENST0000035994716ENSE00000957339chr1:44058128-44058272145PTPRF_HUMAN557-605490--
1.17ENST0000035994717ENSE00000957341chr1:44063419-44063724306PTPRF_HUMAN605-7071030--
1.18bENST0000035994718bENSE00000957342chr1:44064391-44064584194PTPRF_HUMAN707-771650--
1.19ENST0000035994719ENSE00000957343chr1:44067742-4406776827PTPRF_HUMAN772-78090--
1.20bENST0000035994720bENSE00000957344chr1:44069087-44069204118PTPRF_HUMAN781-820401A:1-88
1.21ENST0000035994721ENSE00000957345chr1:44069282-44069860579PTPRF_HUMAN820-10131941A:9-107 (gaps)105
1.22ENST0000035994722ENSE00000957346chr1:44070574-4407067198PTPRF_HUMAN1013-1045330--
1.23ENST0000035994723ENSE00000957347chr1:44070861-44071114254PTPRF_HUMAN1046-1130850--
1.24aENST0000035994724aENSE00000957348chr1:44071200-4407129394PTPRF_HUMAN1130-1161320--
1.25ENST0000035994725ENSE00000957349chr1:44071911-44072129219PTPRF_HUMAN1162-1234730--
1.26aENST0000035994726aENSE00000957350chr1:44072485-44072639155PTPRF_HUMAN1235-1286520--
1.27ENST0000035994727ENSE00000957351chr1:44075054-44075169116PTPRF_HUMAN1286-1325400--
1.29bENST0000035994729bENSE00001720928chr1:44079289-4407938698PTPRF_HUMAN1325-1357330--
1.30ENST0000035994730ENSE00000957369chr1:44083116-44083239124PTPRF_HUMAN1358-1399420--
1.31ENST0000035994731ENSE00001680656chr1:44083407-44083582176PTPRF_HUMAN1399-1457590--
1.32ENST0000035994732ENSE00000957355chr1:44084301-44084420120PTPRF_HUMAN1458-1497400--
1.33ENST0000035994733ENSE00001638469chr1:44084719-44084873155PTPRF_HUMAN1498-1549520--
1.34ENST0000035994734ENSE00000957357chr1:44084959-44085244286PTPRF_HUMAN1549-1644960--
1.35ENST0000035994735ENSE00000957358chr1:44085351-44085529179PTPRF_HUMAN1645-1704600--
1.36aENST0000035994736aENSE00000957359chr1:44085766-44085892127PTPRF_HUMAN1704-1746430--
1.36cENST0000035994736cENSE00001684377chr1:44086125-44086250126PTPRF_HUMAN1747-1788420--
1.37ENST0000035994737ENSE00001754814chr1:44086509-44086663155PTPRF_HUMAN1789-1840520--
1.38ENST0000035994738ENSE00001664652chr1:44086768-44086903136PTPRF_HUMAN1840-1885460--
1.39fENST0000035994739fENSE00001775546chr1:44087606-440893371732PTPRF_HUMAN1886-1907220--

(-) Sequences/Alignments

NMR Structure
   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:107
 aligned with PTPRF_HUMAN | P10586 from UniProtKB/Swiss-Prot  Length:1907

    Alignment length:123
                                   813       823       833       843       853       863       873       883       893       903       913       923   
          PTPRF_HUMAN   804 GDGARSKPKIVTTTGAVPGRPTMMISTTAMNTALLQWHPPKELPGELLGYRLQYCRADEARPNTIDFGKDDQHFTVTGLHKGTTYIFRLAAKNRAGLGEEFEKEIRTPEDLPSGFPQNLHVTG 926
               SCOP domains -------d          2dn7a1 A:8-101 Receptor-type tyrosine-protein phosphatase F, PTPRF                           ------------ SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........----------...eeeeee....eeeeeee..........eeeeeeee......eeeeee....eeeee......eeeeeeeeee..eeeeeeeeeee.......--..----.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE FN3  PDB: -     FN3  PDB: A:9-101 UniProt: 820-914                                                             ---FN3       PROSITE
           Transcript 1 (1) Exon 1.20b       ---------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------Exon 1.21  PDB: A:9-107 (gaps) UniProt: 820-1013 [INCOMPLETE]                                               Transcript 1 (2)
                 2dn7 A   1 GSSGSSGP----------GRPTMMISTTAMNTALLQWHPPKELPGELLGYRLQYCRADEARPNTIDFGKDDQHFTVTGLHKGTTYIFRLAAKNRAGLGEEFEKEIRTPEDLSG--PS----SG 107
                                   | -        10        20        30        40        50        60        70        80        90       100  |  ||  - | 
                                   8          9                                                                                           103  ||  106 
                                                                                                                                             104|      
                                                                                                                                              105      

   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, 1)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DN7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DN7)

(-) Gene Ontology  (26, 34)

NMR Structure(hide GO term definitions)
Chain A   (PTPRF_HUMAN | P10586)
molecular function
    GO:0035373    chondroitin sulfate proteoglycan binding    Interacting selectively and non-covalently with a chondroitin sulfate proteoglycan, any proteoglycan containing chondroitin sulfate as the glycosaminoglycan carbohydrate unit.
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    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: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:0032403    protein complex binding    Interacting selectively and non-covalently with any 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.
    GO:0005001    transmembrane receptor protein tyrosine phosphatase activity    Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
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:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    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:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:1900121    negative regulation of receptor binding    Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor.
    GO:0031102    neuron projection regeneration    The regrowth of neuronal processes such as axons or dendrites in response to their loss or damage.
    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.
    GO:0048679    regulation of axon regeneration    Any process that modulates the frequency, rate or extent of axon regeneration.
    GO:0010975    regulation of neuron projection development    Any process that modulates the rate, frequency or extent of neuron projection development. Neuron projection development is 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:0007185    transmembrane receptor protein tyrosine phosphatase signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses protein tyrosine phosphatase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    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: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:0005887    integral component of plasma membrane    The component of the plasma 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:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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)

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        PTPRF_HUMAN | P105861lar 2dju 2edx 2edy 2yd5 2yd8 4n5u

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