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(-) Description

Title :  SOLUTION STRUCTURE OF RNP DOMAIN IN SYNAPTOJANIN 2
 
Authors :  F. He, Y. Muto, R. Ushikoshi, M. Shirouzu, T. Terada, T. Kigawa, M. Inoue, T. Yabuki, M. Aoki, E. Seki, T. Matsuda, H. Hirota, M. Yoshida N. Kobayashi, A. Tanaka, T. Osanai, Y. Matsuo, O. Ohara, T. Nagase, R. Kikuno, M. Nakayama, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  10 Jun 03  (Deposition) - 10 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Rnp Domain, Synaptojanin 2, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. He, Y. Muto, R. Ushikoshi, M. Shirouzu, T. Terada, T. Kigawa, M. Inoue, T. Yabuki, M. Aoki, E. Seki, T. Matsuda, H. Hirota, M. Yoshida, N. Kobayashi, A. Tanaka, T. Osanai, Y. Matsuo, O. Ohara, T. Nagase, R. Kikuno, M. Nakayama, S. Yokoyama
Solution Structure Of Rnp Domain In Synaptojanin 2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SYNAPTOJANIN 2
    ChainsA
    EC Number3.1.3.36
    EngineeredYES
    Expression System PlasmidP021015-22
    Expression System Vector TypePLASMID
    FragmentRNP DOMAIN
    GeneKAZUSA CDNA HG01551
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS

 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 1UFW)

(-) Sites  (0, 0)

(no "Site" information available for 1UFW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.SYNJ2_HUMAN889-968  1A:15-89

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003555851aENSE00001204730chr6:158402919-158403120202SYNJ2_HUMAN1-43430--
1.2ENST000003555852ENSE00001204724chr6:158438236-15843832287SYNJ2_HUMAN43-72300--
1.4bENST000003555854bENSE00001760278chr6:158449788-158450058271SYNJ2_HUMAN72-162910--
1.6aENST000003555856aENSE00000894238chr6:158454487-158454712226SYNJ2_HUMAN162-237760--
1.7ENST000003555857ENSE00002152303chr6:158464348-15846443184SYNJ2_HUMAN238-265280--
1.8ENST000003555858ENSE00002180718chr6:158475999-15847606062SYNJ2_HUMAN266-286210--
1.9aENST000003555859aENSE00000765575chr6:158480289-15848038597SYNJ2_HUMAN286-318330--
1.10aENST0000035558510aENSE00000765574chr6:158483024-158483196173SYNJ2_HUMAN319-376580--
1.11ENST0000035558511ENSE00002198074chr6:158484823-15848490482SYNJ2_HUMAN376-403280--
1.12ENST0000035558512ENSE00000830232chr6:158485633-158485782150SYNJ2_HUMAN404-453500--
1.13ENST0000035558513ENSE00000830230chr6:158485858-158486023166SYNJ2_HUMAN454-509560--
1.14aENST0000035558514aENSE00000765569chr6:158487476-158487667192SYNJ2_HUMAN509-573650--
1.15ENST0000035558515ENSE00000830228chr6:158489679-15848976082SYNJ2_HUMAN573-600280--
1.16ENST0000035558516ENSE00000830227chr6:158490565-158490705141SYNJ2_HUMAN600-647480--
1.17ENST0000035558517ENSE00000830226chr6:158492634-158492826193SYNJ2_HUMAN647-711650--
1.18ENST0000035558518ENSE00000894235chr6:158495612-158495770159SYNJ2_HUMAN712-764531A:1-44
1.19ENST0000035558519ENSE00000765564chr6:158497658-158497814157SYNJ2_HUMAN765-817530--
1.20bENST0000035558520bENSE00001217886chr6:158499196-158499313118SYNJ2_HUMAN817-856401A:5-73
1.21ENST0000035558521ENSE00002145380chr6:158502141-158502359219SYNJ2_HUMAN856-929741A:8-5548
1.22ENST0000035558522ENSE00000830220chr6:158502464-15850254279SYNJ2_HUMAN929-955271A:55-8127
1.23ENST0000035558523ENSE00000765560chr6:158504461-158504629169SYNJ2_HUMAN956-1012571A:82-95 (gaps)38
1.24ENST0000035558524ENSE00000765559chr6:158505033-158505206174SYNJ2_HUMAN1012-1070590--
1.25ENST0000035558525ENSE00000765558chr6:158507887-158508021135SYNJ2_HUMAN1070-1115460--
1.26ENST0000035558526ENSE00000765557chr6:158509692-158509804113SYNJ2_HUMAN1115-1152380--
1.27ENST0000035558527ENSE00000412332chr6:158510871-158510979109SYNJ2_HUMAN1153-1189370--
1.28ENST0000035558528ENSE00000894234chr6:158513958-158514136179SYNJ2_HUMAN1189-1248600--
1.30cENST0000035558530cENSE00001890001chr6:158516650-1585202083559SYNJ2_HUMAN1249-14962480--

(-) 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:95
 aligned with SYNJ2_HUMAN | O15056 from UniProtKB/Swiss-Prot  Length:1496

    Alignment length:234
                                   769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       949       959       969       979       989    
          SYNJ2_HUMAN   760 KSSGKIFKDFHEGAINFGPTYKYDVGSAAYDTSDKCRTPAWTDRVLWWRKKHPFDKTAGELNLLDSDLDVDTKVRHTWSPGALQYYGRAELQASDHRPVLAIVEVEVQEVDVGARERVFQEVSSFQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQMLVTFADSHSALSVLDVDGMKVKGRAVKIRPKTKDWLKGLREEIIRKRDSMAPVSPTAN 993
               SCOP domains d1uf                                                                          wa_                                          A: Synaptojanin 2                                                                                               SCOP domains
               CATH domains 1ufw                                                                          A00                                          A:1-95  [code=3.30.70.330, no name defined]                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------DUF1866-1ufwA01 A:8-89                                                            ------------------------------ Pfam domains
         Sec.struct. author ...h--------------------------------------------------------------------------hhh-----------------------------------------.........eeeeee....hhhhh...hhhhhhhhhhhhhh....eeeee..eeeee....hhhhhhhhh...ee..eeeeee------------------------..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------RRM  PDB: A:15-89 UniProt: 889-968                                              ------------------------- PROSITE
           Transcript 1 (1) 1.18 Exon 1.19  PDB: - UniProt: 765-817                   --------------------------------------Exon 1.21  PDB: A:8-55 UniProt: 856-929 [INCOMPLETE]                      --------------------------Exon 1.23  PDB: A:82-95 (gaps)         Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------Exon 1.20b  PDB: A:5-7 UniProt: 817-856 ------------------------------------------------------------------------Exon 1.22  PDB: A:55-81    -------------------------------------- Transcript 1 (2)
                 1ufw A   1 GSSG--------------------------------------------------------------------------SSG-----------------------------------------SSFQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQMLVTFADSHSALSVLDVDGMKVKGRAVKIS------------------------GPSSG  95
                               |     -         -         -         -         -         -         -        |6|        -         -         -         -  |     15        25        35        45        55        65        75        85    |    -         -        91    
                               4                                                                          5 7                                         8                                                                                90                       91    

   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  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: RRM (206)

(-) Gene Ontology  (22, 22)

NMR Structure(hide GO term definitions)
Chain A   (SYNJ2_HUMAN | O15056)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0034596    phosphatidylinositol phosphate 4-phosphatase activity    Catalysis of the removal of the 4-phosphate group of a phosphatidylinositol phosphate.
    GO:0052629    phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate + H2O = a 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate + 2 H+.
    GO:0043813    phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity    Catalysis of the reaction: phosphatidylinositol-3,5-bisphosphate + H2O = phosphatidylinositol-3-phosphate + orthophosphate.
    GO:0004438    phosphatidylinositol-3-phosphatase activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 3-phosphate + H2O = 1-phosphatidyl-1D-myo-inositol + phosphate.
    GO:0004439    phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 4-phosphate + phosphate.
    GO:0042578    phosphoric ester hydrolase activity    Catalysis of the reaction: RPO-R' + H2O = RPOOH + R'H. This reaction is the hydrolysis of any phosphoric ester bond, any ester formed from orthophosphoric acid, O=P(OH)3.
    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:0006661    phosphatidylinositol biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidylinositol, any glycophospholipid in which the sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
    GO:0046856    phosphatidylinositol dephosphorylation    The process of removing one or more phosphate groups from a phosphatidylinositol.
    GO:0036092    phosphatidylinositol-3-phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidylinositol-3-phosphate, a phosphatidylinositol monophosphate carrying the phosphate group at the 3-position.
cellular component
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    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: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: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: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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