Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF YEAST FREQUENIN BOUND TO PDTINS 4-KINASE
 
Authors :  J. Ames
Date :  11 Aug 07  (Deposition) - 28 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (15x)
Keywords :  Ef-Hand, Calcium, Ptdins 4-Kinase, Frequenin, Yeast, Lipoprotein, Membrane, Myristate, Nucleus, Phosphorylation, Transferase, Metal Binding Protein/Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Strahl, I. G. Huttner, J. D. Lusin, M. Osawa, D. King, J. Thorner, J. B. Ames
Structural Insights Into Activation Of Phosphatidylinositol 4-Kinase (Pik1) By Yeast Frequenin (Frq1).
J. Biol. Chem. V. 282 30949 2007
PubMed-ID: 17720810  |  Reference-DOI: 10.1074/JBC.M705499200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CALCIUM-BINDING PROTEIN NCS-1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET23A
    Expression System Vector TypePLASMID
    GeneFRQ1, NCS1
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
 
Molecule 2 - PHOSPHATIDYLINOSITOL 4-KINASE PIK1
    ChainsB
    EC Number2.7.1.67
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET23A
    Expression System Vector TypePLASMID
    GenePIK1
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymPI4-KINASE, PTDINS-4-KINASE

 Structural Features

(-) Chains, Units

  
NMR Structure (15x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

NMR Structure (1, 3)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

NMR Structure (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:72 , ASP A:73 , LYS A:74 , ASP A:75 , ASN A:76 , ASN A:77BINDING SITE FOR RESIDUE CA A 500
2AC2SOFTWARETYR A:108 , ASP A:109 , TYR A:115 , ILE A:116 , THR A:117BINDING SITE FOR RESIDUE CA A 501
3AC3SOFTWAREASP A:157 , ASN A:159BINDING SITE FOR RESIDUE CA A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JU0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JU0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JU0)

(-) PROSITE Motifs  (2, 5)

NMR Structure (2, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_2PS50222 EF-hand calcium-binding domain profile.NCS1_YEAST60-95
96-131
144-179
  3A:60-95
A:96-131
A:144-177
2EF_HAND_1PS00018 EF-hand calcium-binding domain.NCS1_YEAST109-121
157-169
  2A:109-121
A:157-169

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR373W1YDR373W.1IV:1222752-1223324573NCS1_YEAST1-1901901A:3-177175

2.1YNL267W1YNL267W.1XIV:140879-1440793201PIK1_YEAST1-106610661B:121-17252

(-) 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:175
 aligned with NCS1_YEAST | Q06389 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:175
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172     
           NCS1_YEAST     3 AKTSKLSKDDLTCLKQSTYFDRREIQQWHKGFLRDCPSGQLAREDFVKIYKQFFPFGSPEDFANHLFTVFDKDNNGFIHFEEFITVLSTTSRGTLEEKLSWAFELYDLNHDGYITFDEMLTIVASVYKMMGSMVTLNEDEATPEMRVKKIFKLMDKNEDGYITLDEFREGSKVDP 177
               SCOP domains d2ju0a_ A: Frequenin (neuronal calcium sensor 1)                                                                                                                                SCOP domains
               CATH domains ---------2ju0A01 A:12-96 EF-hand                                                              2ju0A02 A:97-177 EF-hand                                                          CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------efhand-2ju0A01 A:148-174   --- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------efhand-2ju0A02 A:148-174   --- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------------efhand-2ju0A03 A:148-174   --- Pfam domains (3)
         Sec.struct. author .......hhhhhhhh.....hhhhhhhhhhhhhhhh....eehhhhhhhhhhhh....hhhhhhhhhhhhh.....eehhhhhhhhhhhh.....hhhhhhhhhhh......eeehhhhhhhhhhhhh..hhhhhh.....hhhhhhhhhhhhhh.....eeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------EF_HAND_2  PDB: A:60-95             EF_HAND_2  PDB: A:96-131            ------------EF_HAND_2  PDB: A:144-177          PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------EF_HAND_1    -----------------------------------EF_HAND_1    -------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:3-177 UniProt: 1-190 [INCOMPLETE]                                                                                                                              Transcript 1
                 2ju0 A   3 AKTSKLSKDDLTCLKQSTYFDRREIQQWHKGFLRDCPSGQLAREDFVKIYKQFFPFGSPEDFANHLFTVFDKDNNGFIHFEEFITVLSTTSRGTLEEKLSWAFELYDLNHDGYITFDEMLTIVASVYKMMGSMVTLNEDEATPEMRVKKIFKLMDKNEDGYITLDEFREGSKVDP 177
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172     

Chain B from PDB  Type:PROTEIN  Length:52
 aligned with PIK1_YEAST | P39104 from UniProtKB/Swiss-Prot  Length:1066

    Alignment length:52
                                   130       140       150       160       170  
           PIK1_YEAST   121 ASYGFQVARRVLNNLQTNLFNTSSGSDKNVKIHENVAPALVLSSMIMSAIAF 172
               SCOP domains ---------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
           Pfam domains (1) PI3Ka-2ju0B01         ------------------------------ Pfam domains (1)
           Pfam domains (2) -Pik1-2ju0B02 B:122-171                            - Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhh..................hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: B:121-172 UniProt: 1-1066             Transcript 2
                 2ju0 B 121 ASYGFQVARRVLNNLQTNLFNTSSGSDKNVKIHENVAPALVLSSMIMSAIAF 172
                                   130       140       150       160       170  

   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, 2)

NMR Structure

(-) Pfam Domains  (3, 5)

NMR Structure
(-)
Clan: EF_hand (270)
(-)
Clan: TPR (230)

(-) Gene Ontology  (24, 25)

NMR Structure(hide GO term definitions)
Chain A   (NCS1_YEAST | Q06389)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0008047    enzyme activator activity    Binds to and increases the activity of an enzyme.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0009966    regulation of signal transduction    Any process that modulates the frequency, rate or extent of signal transduction.
cellular component
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0033101    cellular bud membrane    The portion of the plasma membrane surrounding a cellular bud.
    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 B   (PIK1_YEAST | P39104)
molecular function
    GO:0004430    1-phosphatidylinositol 4-kinase activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol + ATP = 1-phosphatidyl-1D-myo-inositol 4-phosphate + ADP + 2 H(+).
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
    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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0046854    phosphatidylinositol phosphorylation    The process of introducing one or more phosphate groups into a phosphatidylinositol, any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol.
    GO:0048015    phosphatidylinositol-mediated signaling    A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0042998    positive regulation of Golgi to plasma membrane protein transport    Any process that activates or increases the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane.
    GO:0050714    positive regulation of protein secretion    Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell.
cellular component
    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:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ju0)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2ju0
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  NCS1_YEAST | Q06389
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  PIK1_YEAST | P39104
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.1.67
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  NCS1_YEAST | Q06389
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PIK1_YEAST | P39104
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NCS1_YEAST | Q063891fpw

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2JU0)