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(-) Description

Title :  HEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE (HGS-HRS) BOUND TO AN IP2 COMPOUND AT 1.68 A RESOLUTION
 
Authors :  E. Williams, P. Canning, L. Shrestha, T. Krojer, M. Vollmar, A. Slowey, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, A. Bullock
Date :  30 May 12  (Deposition) - 13 Jun 12  (Release) - 13 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.68
Chains :  Asym./Biol. Unit :  A
Keywords :  Signaling Protein, Structural Genomics Consortium, Sgc, Signaling (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Williams, P. Canning, L. Shrestha, T. Krojer, M. Vollmar, A. Slowey S. Conway, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, A. Bullock
Crystal Structure Of The Tandem Vhs And Fyve Domains Of Hepatocyte Growth Factor-Regulated Tyrosine Kinase Substrate (Hgs-Hrs) Bound To An Ip2 Compound At 1. 68 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentVHS AND FYVE DOMAINS, RESIDUES 691-915
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2ITP1Ligand/IonPHOSPHORIC ACID MONO-(2,3,4,6-TETRAHYDROXY-5-PHOSPHONOOXY-CYCLOHEXYL) ESTER
3ZN2Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:162 , ALA A:163 , GLU A:164 , LYS A:179BINDING SITE FOR RESIDUE EDO A1224
02AC2SOFTWARECYS A:182 , CYS A:185 , CYS A:212 , CYS A:215BINDING SITE FOR RESIDUE ZN A1225
03AC3SOFTWARECYS A:166 , CYS A:169 , CYS A:190 , CYS A:193BINDING SITE FOR RESIDUE ZN A1226
04AC4SOFTWARETRP A:160 , ARG A:178 , LYS A:179 , HIS A:180 , HIS A:181 , ARG A:183 , ARG A:210 , EDO A:1233 , HOH A:2127 , HOH A:2128 , HOH A:2129 , HOH A:2133 , HOH A:2144 , HOH A:2145 , HOH A:2147 , HOH A:2148BINDING SITE FOR RESIDUE ITP A1227
05AC5SOFTWAREVAL A:102 , ARG A:105 , ASN A:106 , EDO A:1232BINDING SITE FOR RESIDUE EDO A1228
06AC6SOFTWAREPRO A:214 , CYS A:215BINDING SITE FOR RESIDUE EDO A1229
07AC7SOFTWARELYS A:50 , ASN A:54 , GLU A:91 , HOH A:2044BINDING SITE FOR RESIDUE EDO A1230
08AC8SOFTWAREGLN A:18BINDING SITE FOR RESIDUE EDO A1231
09AC9SOFTWAREARG A:105 , LEU A:109 , GLY A:139 , HIS A:140 , VAL A:141 , EDO A:1228BINDING SITE FOR RESIDUE EDO A1232
10BC1SOFTWAREASP A:162 , LYS A:179 , HIS A:181 , ILE A:188 , GLU A:217 , ITP A:1227BINDING SITE FOR RESIDUE EDO A1233
11BC2SOFTWAREGLN A:41 , TYR A:44BINDING SITE FOR RESIDUE EDO A1234

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AVX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AVX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_054154T7SHGS_HUMANPolymorphism753682847AT7S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VHSPS50179 VHS domain profile.HGS_HUMAN15-143  1A:15-143
2ZF_FYVEPS50178 Zinc finger FYVE/FYVE-related type profile.HGS_HUMAN160-220  1A:160-220

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003291381aENSE00001391303chr17:79651020-79651133114HGS_HUMAN1-13131A:6-138
1.2ENST000003291382ENSE00001308807chr17:79652635-7965271985HGS_HUMAN13-41291A:13-4129
1.3ENST000003291383ENSE00001325636chr17:79653342-7965341776HGS_HUMAN41-66261A:41-6626
1.4ENST000003291384ENSE00001314149chr17:79654033-7965412593HGS_HUMAN67-97311A:67-9731
1.5ENST000003291385ENSE00001296740chr17:79655734-79655857124HGS_HUMAN98-139421A:98-13942
1.6ENST000003291386ENSE00001316542chr17:79657212-7965726453HGS_HUMAN139-156181A:139-15618
1.7ENST000003291387ENSE00001292653chr17:79657704-7965777269HGS_HUMAN157-179231A:157-17923
1.8ENST000003291388ENSE00001306492chr17:79658477-79658601125HGS_HUMAN180-221421A:180-22142
1.9ENST000003291389ENSE00001296588chr17:79660533-7966061179HGS_HUMAN221-247271A:221-2233
1.10ENST0000032913810ENSE00001313160chr17:79660684-7966078299HGS_HUMAN248-280330--
1.11ENST0000032913811ENSE00001292556chr17:79660900-7966099596HGS_HUMAN281-312320--
1.12ENST0000032913812ENSE00001314367chr17:79661845-7966188339HGS_HUMAN313-325130--
1.13ENST0000032913813ENSE00001303643chr17:79661954-79662097144HGS_HUMAN326-373480--
1.14ENST0000032913814ENSE00001321161chr17:79662194-7966225360HGS_HUMAN374-393200--
1.15ENST0000032913815ENSE00001299855chr17:79662816-79663029214HGS_HUMAN394-465720--
1.16bENST0000032913816bENSE00001299623chr17:79663387-79663559173HGS_HUMAN465-522580--
1.17ENST0000032913817ENSE00001301435chr17:79663637-79663777141HGS_HUMAN523-569470--
1.18aENST0000032913818aENSE00001421749chr17:79663854-79664028175HGS_HUMAN570-628590--
1.19ENST0000032913819ENSE00001300174chr17:79667497-79667630134HGS_HUMAN628-672450--
1.20ENST0000032913820ENSE00001320441chr17:79667725-79667844120HGS_HUMAN673-712400--
1.21ENST0000032913821ENSE00001296545chr17:79668075-7966816187HGS_HUMAN713-741290--
1.22aENST0000032913822aENSE00001319441chr17:79668538-79669143606HGS_HUMAN742-777360--

(-) 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:218
 aligned with HGS_HUMAN | O14964 from UniProtKB/Swiss-Prot  Length:777

    Alignment length:218
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215        
            HGS_HUMAN     6 GTFERLLDKATSQLLLETDWESILQICDLIRQGDTQAKYAVNSIKKKVNDKNPHVALYALEVMESVVKNCGQTVHDEVANKQTMEELKDLLKRQVEVNVRNKILYLIQAWAHAFRNEPKYKVVQDTYQIMKVEGHVFPEFKESDAMFAAERAPDWVDAEECHRCRVQFGVMTRKHHCRACGQIFCGKCSSKYSTIPKFGIEKEVRVCEPCYEQLNRKA 223
               SCOP domains d4avxa1 A:6-147 automated matches                                                                                                             d4avxa2 A:148-223 automated matches                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.......hhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhh............................ee......eehhhhh.eeeeehhhheeeeeeehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -S------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------VHS  PDB: A:15-143 UniProt: 15-143                                                                                               ----------------ZF_FYVE  PDB: A:160-220 UniProt: 160-220                     --- PROSITE
           Transcript 1 (1) 1.1a    ---------------------------Exon 1.3  PDB: A:41-66    Exon 1.4  PDB: A:67-97         Exon 1.5  PDB: A:98-139 UniProt: 98-139   -----------------Exon 1.7  PDB: A:157-17Exon 1.8  PDB: A:180-221 UniProt: 180-221 -- Transcript 1 (1)
           Transcript 1 (2) -------Exon 1.2  PDB: A:13-41       -------------------------------------------------------------------------------------------------Exon 1.6          ----------------------------------------------------------------1.9 Transcript 1 (2)
                 4avx A   6 GTFERLLDKATSQLLLETDWESILQICDLIRQGDTQAKYAVNSIKKKVNDKNPHVALYALEVMESVVKNCGQTVHDEVANKQTMEELKDLLKRQVEVNVRNKILYLIQAWAHAFRNEPKYKVVQDTYQIMKVEGHVFPEFKESDAMFAAERAPDWVDAEECHRCRVQFGVMTRKHHCRACGQIFCGKCSSKYSTIPKFGIEKEVRVCEPCYEQLNRKA 223
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215        

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AVX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AVX)

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HGS_HUMAN | O14964)
molecular function
    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).
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
biological process
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    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:0006886    intracellular protein transport    The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
    GO:0010324    membrane invagination    The infolding of a membrane.
    GO:0036258    multivesicular body assembly    The aggregation, arrangement and bonding together of a set of components to form a multivesicular body, a type of late endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm.
    GO:0046426    negative regulation of JAK-STAT cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of the JAK-STAT signaling pathway activity.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0042059    negative regulation of epidermal growth factor receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
    GO:1903543    positive regulation of exosomal secretion    Any process that activates or increases the frequency, rate or extent of exosomal secretion.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0072657    protein localization to membrane    A process in which a protein is transported to, or maintained in, a specific location in a membrane.
    GO:0006622    protein targeting to lysosome    The process of directing proteins towards the lysosome using signals contained within the protein.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0043405    regulation of MAP kinase activity    Any process that modulates the frequency, rate or extent of MAP kinase activity.
    GO:0042176    regulation of protein catabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    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:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0033565    ESCRT-0 complex    A protein complex required for the recycling of Golgi proteins, formation of lumenal membranes and sorting of ubiquitinated proteins into those membranes. This complex includes Vps1p and Hse1p in yeast and the Hrs and STAM proteins in mammals.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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: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: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.
    GO:0032585    multivesicular body membrane    The lipid bilayer surrounding a multivesicular body.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HGS_HUMAN | O149642d3g 3f1i 3obq 3zyq

(-) Related Entries Specified in the PDB File

2d3g DOUBLE SIDED UBIQUITIN BINDING OF HRS-UIM
3zyq CRYSTAL STRUCTURE OF THE TANDEM VHS AND FYVE DOMAINS OF HEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE (HGS-HRS) AT 1.48 A RESOLUTION