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(-) Description

Title :  CRYSTAL STRUCTURE OF THE VHS AND FYVE TANDEM DOMAINS OF HRS, A PROTEIN INVOLVED IN MEMBRANE TRAFFICKING AND SIGNAL TRANSDUCTION
 
Authors :  Y. Mao, A. Nickitenko, X. Duan, T. E. Lloyd, M. N. Wu, H. Bellen, F. A. Quiocho
Date :  21 Jan 00  (Deposition) - 06 Mar 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hrs, Vhs, Fyve, Zinc Finger, Superhelix, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Mao, A. Nickitenko, X. Duan, T. E. Lloyd, M. N. Wu, H. Bellen, F. A. Quiocho
Crystal Structure Of The Vhs And Fyve Tandem Domains Of Hrs, A Protein Involved In Membrane Trafficking And Signal Transduction.
Cell(Cambridge, Mass. ) V. 100 447 2000
PubMed-ID: 10693761  |  Reference-DOI: 10.1016/S0092-8674(00)80680-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTYB1
    Expression System Taxid562
    FragmentN-TERMINAL VHS AND FYVE TANDEM DOMAINS
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
    SynonymHRS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:164 , CYS A:167 , CYS A:188 , CYS A:191BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWARECYS A:180 , CYS A:183 , CYS A:210 , CYS A:213BINDING SITE FOR RESIDUE ZN A 402
3AC3SOFTWARETRP A:158 , ARG A:176 , HIS A:178 , HIS A:179 , ARG A:181 , ARG A:208 , HOH A:463 , HOH A:498 , HOH A:520 , HOH A:598BINDING SITE FOR RESIDUE CIT A 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VHSPS50179 VHS domain profile.HRS_DROME13-141  1A:13-141
2ZF_FYVEPS50178 Zinc finger FYVE/FYVE-related type profile.HRS_DROME158-218  1A:158-218
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VHSPS50179 VHS domain profile.HRS_DROME13-141  2A:13-141
2ZF_FYVEPS50178 Zinc finger FYVE/FYVE-related type profile.HRS_DROME158-218  2A:158-218

(-) Exons   (0, 0)

(no "Exon" information available for 1DVP)

(-) Sequences/Alignments

Asymmetric 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:217
 aligned with HRS_DROME | Q960X8 from UniProtKB/Swiss-Prot  Length:760

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
            HRS_DROME     1 MFRSSFDKNLENATSHLRLEPDWPSILLICDEINQKDVTPKNAFAAIKKKMNSPNPHSSCYSLLVLESIVKNCGAPVHEEVFTKENCEMFSSFLESTPHENVRQKMLELVQTWAYAFRSSDKYQAIKDTMTILKAKGHTFPELREADAMFTADTAPNWADGRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTAKQCPLPKYGIEKEVRVCDGCFAALQRPTSG 223
               SCOP domains d1dvpa1 A:1-145 Hrs                                                                                                                              ---d1dvpa2 A:149-220 Hrs                                                       SCOP domains
               CATH domains -1dvpA01 A:2-141  [code=1.25.40.90, no name defined]                                                                                         ------------1dvpA02 A:154-219 Zinc/RING finger domain, C3HC4 (zinc finger)    ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh......hhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.........---.............................ee......ee......eeeeehhhheeeeeeehhhhhhhhhh---h Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------VHS  PDB: A:13-141 UniProt: 13-141                                                                                               ----------------ZF_FYVE  PDB: A:158-218 UniProt: 158-218                     ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dvp A   1 MFRSSFCKNLENATSHLRLEPDWPSILLICDEINQKDVTPKNAFAAIKKKMNSPNPHSSCYSLLVLESIVKNCGAPVHEEVFTKENCEMFSSFLESTPHENVRQKMLELVQTWAYAFRSSDKYQAIKDTMTILKAKGHTFPELRE---MFTADTAPNWADGRVCHRCRVEFTFTNRKHHCRNCGQVFCGQCTAKQCPLPKYGIEKEVRVCDGCFAALQR---G 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    |  150       160       170       180       190       200       210        |-  |
                                                                                                                                                                          145 149                                                                   219 220

   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 Unit

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DVP)

(-) Gene Ontology  (35, 35)

Asymmetric Unit(hide GO term definitions)
Chain A   (HRS_DROME | Q960X8)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
biological process
    GO:0007298    border follicle cell migration    The directed movement of a border cell through the nurse cells to reach the oocyte. An example of this is found in Drosophila melanogaster.
    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: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:0008333    endosome to lysosome transport    The directed movement of substances from endosomes to lysosomes.
    GO:0032509    endosome transport via multivesicular body sorting pathway    The directed movement of substances from endosomes to lysosomes or vacuoles by a pathway in which molecules are sorted into multivesicular bodies, which then fuse with the target compartment.
    GO:0006887    exocytosis    A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
    GO:1990182    exosomal secretion    The process whereby a membrane-bounded vesicle is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane.
    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:0033619    membrane protein proteolysis    The proteolytic cleavage of a transmembrane protein leading to the release of its intracellular or ecto-domains.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    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:0001933    negative regulation of protein phosphorylation    Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
    GO:0016322    neuron remodeling    The developmentally regulated remodeling of neuronal projections such as pruning to eliminate the extra dendrites and axons projections set up in early stages of nervous system development.
    GO:0007269    neurotransmitter secretion    The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium regualated exocytosis during synaptic transmission.
    GO:0045752    positive regulation of Toll signaling pathway    Any process that activates or increases the frequency, rate or extent of the Tl signaling pathway.
    GO:0045743    positive regulation of fibroblast growth factor receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of fibroblast growth factor receptor signaling pathway activity.
    GO:0031398    positive regulation of protein ubiquitination    Any process that activates or increases the frequency, rate or extent of the addition of ubiquitin groups to a protein.
    GO:0008593    regulation of Notch signaling pathway    Any process that modulates the frequency, rate or extent of the Notch signaling pathway.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
    GO:2000274    regulation of epithelial cell migration, open tracheal system    Any process that modulates the frequency, rate or extent of epithelial cell migration, open tracheal system.
    GO:0016079    synaptic vesicle exocytosis    Fusion of intracellular membrane-bounded vesicles with the pre-synaptic membrane of the neuronal cell resulting in release of neurotransmitter into the synaptic cleft.
    GO:0016082    synaptic vesicle priming    A process that converts synaptic vesicles to a state of competence for calcium triggered fusion with the active zone membrane by bringing the two membranes into very close proximity. Priming typically (but not always) occurs after docking (Jahn and Fasshauer, 2012). Primed vesicles are also capable of spontaneously fusing with the active zone membrane.
    GO:0008293    torso signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to torso (a receptor tyrosine kinase) on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    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: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:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    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:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0005770    late endosome    A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0008021    synaptic vesicle    A secretory organelle, typically 50 nm in diameter, of presynaptic nerve terminals; accumulates in high concentrations of neurotransmitters and secretes these into the synaptic cleft by fusion with the 'active zone' of the presynaptic plasma membrane.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1vfy 1VFY CONTAINS A YEAST HOMOLOGUE OF FYVE DOMAIN