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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FYVE DOMAIN OF ENDOFIN (ZFYVE16) AT 1.1A RESOLUTION
 
Authors :  A. Chaikuad, E. Williams, K. Guo, C. Sanvitale, G. Berridge, T. Krojer, J. R. C. Muniz, P. Canning, C. Phillips, A. Shrestha, F. Von Delft, J. W C. H. Arrowsmith, A. M. Edwards, C. Bountra, A. Bullock, Structural G Consortium (Sgc)
Date :  30 Jul 11  (Deposition) - 31 Aug 11  (Release) - 31 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.09
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics Consortium, Sgc, Zinc Finger, Lipid Binding Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Chaikuad, E. Williams, K. Guo, C. Sanvitale, G. Berridge, T. Krojer J. R. C. Muniz, P. Canning, C. Phillips, A. Shrestha, F. Von Delft, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, C. Bountra, A. Bullock, Structural Genomics Consortium (Sgc)
Crystal Structure Of The Fyve Domain Of Endofin (Zfyve16) A 1. 1A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ZINC FINGER FYVE DOMAIN-CONTAINING PROTEIN 16
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC-ZB
    Expression System StrainROSETTA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentFYVE DOMAIN (UNP RESIDUES 733-820)
    GeneKIAA0305, ZFYVE16
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymENDOFIN, ENDOSOME-ASSOCIATED FYVE DOMAIN PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2ZN2Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:753 , CYS A:756 , CYS A:777 , CYS A:780BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWARECYS A:769 , CYS A:772 , CYS A:797 , CYS A:800BINDING SITE FOR RESIDUE ZN A 2
3AC3SOFTWAREHOH A:26 , HOH A:52 , HOH A:63 , HOH A:82 , MET A:754 , ASN A:755 , GLN A:757 , PHE A:762BINDING SITE FOR RESIDUE EDO A 821

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T7L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3T7L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T7L)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_FYVEPS50178 Zinc finger FYVE/FYVE-related type profile.ZFY16_HUMAN747-805  1A:747-805

(-) Exons   (0, 0)

(no "Exon" information available for 3T7L)

(-) 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:74
 aligned with ZFY16_HUMAN | Q7Z3T8 from UniProtKB/Swiss-Prot  Length:1539

    Alignment length:74
                                   744       754       764       774       784       794       804    
          ZFY16_HUMAN   735 LVLGQKQPTWVPDSEAPNCMNCQVKFTFTKRRHHCRACGKVFCGVCCNRKCKLQYLEKEARVCVVCYETISKAQ 808
               SCOP domains d3t7la_ A: automated matches                                               SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhh................ee......eehhhhh.eeee......eeeehhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------ZF_FYVE  PDB: A:747-805 UniProt: 747-805                   --- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 3t7l A 735 LVLGQKQPTWVPDSEAPNCMNCQVKFTFTKRRHHCRACGKVFCGVCCNRKCKLQYLEKEARVCVVCYETISKAQ 808
                                   744       754       764       774       784       794       804    

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T7L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T7L)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ZFY16_HUMAN | Q7Z3T8)
molecular function
    GO:0005545    1-phosphatidylinositol binding    Interacting selectively and non-covalently with phosphatidylinositol, any glycophospholipid with its sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005547    phosphatidylinositol-3,4,5-trisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3,4,5-trisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3', 4' and 5' positions.
    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:0008565    protein transporter activity    Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
    GO:0030509    BMP signaling pathway    A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0016197    endosomal transport    The directed movement of substances into, out of, or mediated by an endosome, a membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation.
    GO:0006622    protein targeting to lysosome    The process of directing proteins towards the lysosome using signals contained within the protein.
    GO:0030100    regulation of endocytosis    Any process that modulates the frequency, rate or extent of endocytosis.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0016050    vesicle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0031901    early endosome membrane    The lipid bilayer surrounding an early endosome.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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