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(-) Description

Title :  STRACTURAL INSIGHT INTO THE INTERACTION BETWEEN ESCRT-III AND VPS4
 
Authors :  T. Obita, O. Perisic, S. Ghazi-Tabatabai, S. Saksena, S. D. Emr, R. L. Wi
Date :  23 Jul 07  (Deposition) - 16 Oct 07  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein Transport, Vacuole, Endosome, Transport, Escrt-Iii, Mvb, Vps2, Vps4, Skd1, Vps4B, Vps4A, Chmp2B, Chmp2A, Nucleotide-Binding, Aaa-Atpase, Atp-Binding, Multivesicular, Vacuolar Protein Sorting (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Obita, S. Saksena, S. Ghazi-Tabatabai, D. J. Gill, O. Perisic, S. D. Emr, R. L. Williams
Structural Basis For Selective Recognition Of Escrt-Iii By The Aaa Atpase Vps4
Nature V. 449 735 2007
PubMed-ID: 17928861  |  Reference-DOI: 10.1038/NATURE06171

(-) Compounds

Molecule 1 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4
    ChainsA
    EC Number3.6.4.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPOPTG
    Expression System StrainC41(DE3)
    Expression System Taxid562
    FragmentMIT DOMAIN RESIUDES 1-82
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymVPS4, PROTEIN END13, DOA4-INDEPENDENT DEGRADATION PROTEIN 6, VACUOLAR PROTEIN-TARGETING PROTEIN 10
 
Molecule 2 - DOA4-INDEPENDENT DEGRADATION PROTEIN 4
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPOPTG
    Expression System StrainC41(DE3)
    Expression System Taxid562
    FragmentC-TERMINAL FRAGMENT RESIDUES 102-151
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymVACUOLAR PROTEIN SORTING- ASSOCIATED PROTEIN 2, VPS2, VACUOLAR PROTEIN-TARGETING PROTEIN 14

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:15 , MSE B:201 , GLY B:202 , HOH B:1008 , HOH B:1009BINDING SITE FOR RESIDUE SO4 B1232

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V6X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V6X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V6X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V6X)

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YKL002W1YKL002W.1XI:437421-43748060DID4_YEAST1-20200--
1.2YKL002W2YKL002W.2XI:437549-438187639DID4_YEAST21-2322121B:181-231 (gaps)51

2.1YPR173C1YPR173C.1XVI:887833-8865201314VPS4_YEAST1-4374371A:1-8080

(-) 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:82
 aligned with VPS4_YEAST | P52917 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:82
                              1                                                                               
                              |      8        18        28        38        48        58        68        78  
           VPS4_YEAST     - --MSTGDFLTKGIELVQKAIDLDTATQYEEAYTAYYNGLDYLMLALKYEKNPKSKDLIRAKFTEYLNRAEQLKKHLESEEAN  80
               SCOP domains d2v6xa_ A: automated matches                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains -------MIT-2v6xA01 A:6-74                                                   ------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
               Transcript 2 --Exon 2.1  PDB: A:1-80 UniProt: 1-437 [INCOMPLETE]                                Transcript 2
                 2v6x A  -1 SHmSTGDFLTKGIELVQKAIDLDTATQYEEAYTAYYNGLDYLmLALKYEKNPKSKDLIRAKFTEYLNRAEQLKKHLESEEAN  80
                              |      8        18        28        38  |     48        58        68        78  
                              1-MSE                                  41-MSE                                   

Chain B from PDB  Type:PROTEIN  Length:41
 aligned with DID4_YEAST | P36108 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:51
                                   190       200       210       220       230 
           DID4_YEAST   181 SQLQSTPQNLVSNAPIAETAMGIPEPIGAGSEFHGNPDDDLQARLNTLKKQ 231
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --Snf7-2v6x---------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh...hhhhhh.....----------.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: B:181-231 (gaps) UniProt: 21-232     Transcript 1
                 2v6x B 181 HmLQSTPQNLVSNAPIAETAmGIAEP----------PDDDLQARLNTLKKQ 231
                             |     190       200|    |   -      |220       230 
                             |                201-MSE6        217              
                           182-MSE                                             

   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 2V6X)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: PspA (1)

(-) Gene Ontology  (28, 37)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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.

Chain B   (DID4_YEAST | P36108)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    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).
biological process
    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: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: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:0007034    vacuolar transport    The directed movement of substances into, out of or within a vacuole.
cellular component
    GO:0000815    ESCRT III complex    An endosomal sorting complex required for transport. Consists of two soluble subcomplexes of highly charged coiled-coil proteins and is required for sorting and/or concentration of multivesicular body (MVB) cargoes.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        VPS4_YEAST | P529172qp9 2qpa 2rko 3eie 3eih 3mhv 4niq 5fvk 5fvl 5uie

(-) Related Entries Specified in the PDB File

1wr0 STRUCTURAL CHARACTERIZATION OF THE MIT DOMAIN FROM HUMANVPS4B
1xwi CRYSTAL STRUCTURE OF VPS4B
1yxr NMR STRUCTURE OF VPS4A MIT DOMAIN