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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE SKD1/VPS4B APO-FORM
 
Authors :  M. Inoue, M. Kawasaki, H. Kamikubo, M. Kataoka, R. Kato, T. Yoshimori, S. Wakatsuki
Date :  08 Oct 07  (Deposition) - 07 Oct 08  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Skd1, Vps4B, Aaa Atpase, Atp-Binding, Membrane, Nucleotide-Binding, Phosphorylation, Protein Transport, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Inoue, H. Kamikubo, M. Kataoka, R. Kato, T. Yoshimori, S. Wakatsuki M. Kawasaki
Nucleotide-Dependent Conformational Changes And Assembly Of The Aaa Atpase Skd1/Vps4B
Traffic V. 9 2180 2008
PubMed-ID: 18796009  |  Reference-DOI: 10.1111/J.1600-0854.2008.00831.X

(-) Compounds

Molecule 1 - VACUOLAR PROTEIN SORTING-ASSOCIATING PROTEIN 4B
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPPROEXHTB
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSKD1
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymPROTEIN SKD1, SUPPRESSOR OF K+, TRANSPORT GROWTH DEFECT 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2ZAM)

(-) Sites  (0, 0)

(no "Site" information available for 2ZAM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:227 -Pro A:228

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AAAPS00674 AAA-protein family signature.VPS4B_MOUSE272-291  1A:272-291

(-) Exons   (0, 0)

(no "Exon" information available for 2ZAM)

(-) 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:308
 aligned with VPS4B_MOUSE | P46467 from UniProtKB/Swiss-Prot  Length:444

    Alignment length:322
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442  
          VPS4B_MOUSE   123 AIVIERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRKTDGYSGADISIIVRDALMQPVRKVQSATHFKKVRGPSRADPNCIVNDLLTPCSPGDPGAIEMTWMDVPGDKLLEPVVSMWDMLRSLSSTKPTVNEQDLLKLKKFTEDFGQEG 444
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------AAA-2zamA01 A:170-300                                                                                                              -------------------------------------------------------------------------------Vps4_C-2zamA02 A:380-441                                      --- Pfam domains
         Sec.struct. author .........hhhhh..hhhhhhhhhhhhhhhhhhhhhh........eeeee.....hhhhhhhhhhhhh...eeeee.......-----..hhhhhhhhhhhhh..eeeeee....---------...hhhhhhhhhhhhhh.......eeeeeee......hhhhhhhh.eeee.....hhhhhhhhhhhhh......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeeeeeeee.......ee................hhhhhhhhhh......hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------AAA  PDB: A:272-291 --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zam A 123 AIVIERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVS-----SEKLVKNLFQLARENKPSIIFIDEIDS---------SEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRRRFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRKTDGYSGADISIIVRDALMQPVRKVQSATHFKKVRGPSRADPNCIVNDLLTPCSPGDPGAIEMTWMDVPGDKLLEPVVSMWDMLRSLSSTKPTVNEQDLLKLKKFTEDFGQEG 444
                                   132       142       152       162       172       182       192       202   |   212       222       232     |   -     | 252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442  
                                                                                                             206   212                       238       248                                                                                                                                                                                                    

   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 2ZAM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZAM)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (53, 53)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VPS4B_MOUSE | P46467)
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:0042623    ATPase activity, coupled    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction directly drives some other reaction, for example ion transport across a membrane.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    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:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0000920    cell separation after cytokinesis    The process of physically separating progeny cells after cytokinesis; this may involve enzymatic digestion of septum or cell wall components.
    GO:0030301    cholesterol transport    The directed movement of cholesterol, cholest-5-en-3-beta-ol, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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: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:0007032    endosome organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of endosomes.
    GO:0032510    endosome to lysosome transport via multivesicular body sorting pathway    The directed movement of substances from endosomes to lysosomes by a pathway in which molecules are sorted into multivesicular bodies, which then fuse with the lysosome.
    GO:0061738    late endosomal microautophagy    The autophagy process by which cytosolic proteins targeted for degradation are tagged with a chaperone and are directly transferred into and degraded in a late endosomal compartment.
    GO:0007080    mitotic metaphase plate congression    The cell cycle process in which chromosomes are aligned at the metaphase plate, a plane halfway between the poles of the mitotic spindle, during mitosis.
    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:0060548    negative regulation of cell death    Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
    GO:1903542    negative regulation of exosomal secretion    Any process that stops, prevents or reduces the frequency, rate or extent of exosomal secretion.
    GO:0006997    nucleus organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus.
    GO:0010971    positive regulation of G2/M transition of mitotic cell cycle    Any process that increases the rate or extent of progression from G2 phase to M phase of the mitotic cell cycle.
    GO:1903724    positive regulation of centriole elongation    Any process that activates or increases the frequency, rate or extent of centriole elongation.
    GO:1903543    positive regulation of exosomal secretion    Any process that activates or increases the frequency, rate or extent of exosomal secretion.
    GO:1903902    positive regulation of viral life cycle    Any process that activates or increases the frequency, rate or extent of viral life cycle.
    GO:0048524    positive regulation of viral process    Any process that activates or increases the frequency, rate or extent of a multi-organism process in which a virus is a participant.
    GO:1902188    positive regulation of viral release from host cell    Any process that activates or increases the frequency, rate or extent of viral release from host cell.
    GO:0006813    potassium ion transport    The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0051261    protein depolymerization    The process in which protein polymers, compounds composed of a large number of component monomers, are broken down. Depolymerization occurs by the successive removal of monomers from an existing poly- or oligomeric 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:0010824    regulation of centrosome duplication    Any process that modulates the frequency, rate or extent of centrosome duplication. Centrosome duplication is the replication of a centrosome, a structure comprised of a pair of centrioles and peri-centriolar material from which a microtubule spindle apparatus is organized.
    GO:1901673    regulation of mitotic spindle assembly    Any process that modulates the frequency, rate or extent of mitotic spindle assembly.
    GO:0050792    regulation of viral process    Any process that modulates the rate or extent of the viral life cycle, the set of processes by which a virus reproduces and spreads among hosts.
    GO:0033993    response to lipid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipid stimulus.
    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:0043162    ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway    The chemical reactions and pathways resulting in the breakdown of a protein or peptide covalently tagged with ubiquitin, via the multivesicular body (MVB) sorting pathway; ubiquitin-tagged proteins are sorted into MVBs, and delivered to a lysosome/vacuole for degradation.
    GO:0090611    ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway    The chemical reactions and pathways resulting in the breakdown of a protein or peptide, via the multivesicular body (MVB) sorting pathway; proteins are sorted into MVBs, and delivered to a lysosome/vacuole for degradation. This process is independent of ubiquitination.
    GO:0039702    viral budding via host ESCRT complex    Viral budding which uses a host ESCRT protein complex, or complexes, to mediate the budding process.
    GO:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
    GO:0090543    Flemming body    A cell part that is the central region of the midbody characterized by a gap in alpha-tubulin staining. It is a dense structure of antiparallel microtubules from the central spindle in the middle of the intercellular bridge.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    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:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    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:0031902    late endosome membrane    The lipid bilayer surrounding a late 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.
    GO:0000922    spindle pole    Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.

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 Related Entries

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

UniProtKB/Swiss-Prot
        VPS4B_MOUSE | P464672zan 2zao

(-) Related Entries Specified in the PDB File

1xwi MODEL IN MOLECULAR REPLACEMENT
2zan
2zao