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(-) Description

Title :  CRYSTAL STRUCTURE OF S.CEREVISIAE VPS4
 
Authors :  J. Xiao, Z. Xu
Date :  23 Jul 07  (Deposition) - 09 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  X
Keywords :  Atpase Domain, Beta Domain, C-Terminal Helix, Atp-Binding, Endosome, Nucleotide-Binding, Protein Transport, Transport, Vacuole (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Xiao, H. Xia, K. Yoshino-Koh, J. Zhou, Z. Xu
Structural Characterization Of The Atpase Reaction Cycle Of Endosomal Aaa Protein Vps4.
J. Mol. Biol. V. 374 655 2007
PubMed-ID: 17949747  |  Reference-DOI: 10.1016/J.JMB.2007.09.067

(-) Compounds

Molecule 1 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4
    ChainsX
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPSJ3
    Expression System StrainROSETTA(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES: 83-437
    GeneVPS4, CSC1, DID6, END13, GRD13, VPL4, VPT10
    MutationYES
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymPROTEIN END13, DOA4-INDEPENDENT DEGRADATION PROTEIN 6, VACUOLAR PROTEIN-TARGETING PROTEIN 10

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit X

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CD2Ligand/IonCADMIUM ION
2SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU X:392 , ASP X:394BINDING SITE FOR RESIDUE CD X 601
2AC2SOFTWAREGLU X:189 , ASP X:390BINDING SITE FOR RESIDUE CD X 603
3AC3SOFTWAREGLY X:176 , THR X:177 , GLY X:178 , LYS X:179 , ASN X:277BINDING SITE FOR RESIDUE SO4 X 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QP9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys X:225 -Pro X:226

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QP9)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AAAPS00674 AAA-protein family signature.VPS4_YEAST270-289  1X:270-289

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPR173C1YPR173C.1XVI:887833-8865201314VPS4_YEAST1-4374371X:129-433 (gaps)305

(-) 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 X from PDB  Type:PROTEIN  Length:288
 aligned with VPS4_YEAST | P52917 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:305
                                   138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428     
           VPS4_YEAST   129 NVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDEVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIRKIQSATHFKDVSTEDDETRKLTPCSPGDDGAIEMSWTDIEADELKEPDLTIKDFLKAIKSTRPTVNEDDLLKQEQFTRDFG 433
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qp9X01 X:129-298,X:416-433 P-loop containing nucleotide triphosphate hydrolas   es                                                                                       -------------------------------------------------------------------     ---------------------------------------------2qp9X01            CATH domains
               Pfam domains ----------------------------------------AAA-2qp9X01 X:169-298                                                                                                             -------------------------------------------------------------------     -Vps4_C-2qp9X02 X:372-433                                       Pfam domains
         Sec.struct. author ..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........eeee.....hhhhhhhhhhhhhh.eeeeeehhhhhh..---hhhhhhhhhhhhhhh..eeeeeehhhhhh.------.hhhhhhhhhhhhhhhhh.---..eeeeeee.hhhhhhhhhhhh..eeee....hhhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.eeee...-----..eeee......eee.hhhhhhhhhh.....hhhhhhhhhhhh....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------AAA  PDB: X:270-289 ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: X:129-433 (gaps) UniProt: 1-437 [INCOMPLETE]                                                                                                                                                                                                                                                       Transcript 1
                 2qp9 X 129 NVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSKW---SEKLVKQLFAMARENKPSIIFIDQVDALTG------SEASRRIKTELLVQMNGVG---QGVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPSVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIRKIQSATHFKDVST-----RKLTPSSPGDDGAIEMSWTDIEADELKEPDLTIKDFLKAIKSTRPTVNEDDLLKQEQFTRDFG 433
                                   138       148       158       168       178       188       198       | - |     218       228       238|      248       258     | 268       278       288       298       308       318       328       338       348       358      |  -  |    378       388       398       408       418       428     
                                                                                                       206 210                          239    246               264 268                                                                                              365   371                                                              

   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  (0, 0)

(no "SCOP Domain" information available for 2QP9)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (VPS4_YEAST | P52917)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0008568    microtubule-severing ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate. Catalysis of the severing of a microtubule at a specific spot along its length, coupled to the hydrolysis of ATP.
    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: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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0031122    cytoplasmic microtubule organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures formed of microtubules and associated proteins in the cytoplasm of a cell.
    GO:0070676    intralumenal vesicle formation    The invagination of the endosome membrane and resulting formation of a vesicle within the lumen of the endosome.
    GO:0045324    late endosome to vacuole transport    The directed movement of substances from late endosomes to the vacuole. In yeast, after transport to the prevacuolar compartment, endocytic content is delivered to the late endosome and on to the vacuole. This pathway is analogous to endosome to lysosome transport.
    GO:0032511    late endosome to vacuole transport via multivesicular body sorting pathway    The directed movement of substances from endosomes to vacuoles by a pathway in which molecules are sorted into multivesicular bodies, which then fuse with the vacuole.
    GO:0016236    macroautophagy    The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0045053    protein retention in Golgi apparatus    The retention of proteins within the Golgi apparatus. Golgi-localized carbohydrate-modifying enzymes have a short N-terminal domain that faces the cytosol, a single transmembrane alpha helix, and a large C-terminal domain that faces the Golgi lumen and that contains the catalytic site. How the membrane-spanning alpha helix in a Golgi enzyme causes its localization and prevents its movement to the plasma membrane is not known.
    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:0016125    sterol metabolic process    The chemical reactions and pathways involving sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
    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.
    GO:0007033    vacuole organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vacuole.
cellular component
    GO:1990621    ESCRT IV complex    An ESCRT complex that has AAA-ATPase activity and is involved in ESCRT-mediated intralumenal vesicle formation and the final stages of cytokinesis. The complex catalyzes disassembly of the ESCRT III filament around the neck of the budding vesicle in an ATP-driven reaction, resulting in membrane scission and recycling of the ESCRT III components back to the cytosol. In yeast, it is formed by the AAA ATPase Vps4 and its cofactor Vta1.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        VPS4_YEAST | P529172qpa 2rko 2v6x 3eie 3eih 3mhv 4niq 5fvk 5fvl 5uie

(-) Related Entries Specified in the PDB File

2qpa STRUCTURE OF S.CEREVISIAE VPS4 IN THE PRESENCE OF ADP