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(-) Description

Title :  CRYSTAL STRUCTURE OF S.CEREVISIAE VTA1 N-TERMINAL DOMAIN
 
Authors :  J. Xiao, H. Xia, J. Zhou, Z. Xu
Date :  16 Oct 07  (Deposition) - 22 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mit Motif, Cytoplasm, Endosome, Lipid Transport, Membrane, Protein Transport, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Xiao, H. Xia, J. Zhou, I. F. Azmi, B. A. Davies, D. J. Katzmann, Z. Xu
Structural Basis Of Vta1 Function In The Multivesicular Body Sorting Pathway.
Dev. Cell V. 14 37 2008
PubMed-ID: 18194651  |  Reference-DOI: 10.1016/J.DEVCEL.2007.10.013
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VTA1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN
    Gene: VTA1
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: VPS20-ASSOCIATED PROTEIN 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2RKK)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YLR181C1YLR181C.1XII:517672-516680993VTA1_YEAST1-3303302A:1-167 (gaps)
B:1-167 (gaps)		167
167

(-) 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:157
 aligned with VTA1_YEAST | Q06263 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:168
                             1                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159        
           VTA1_YEAST     - -MASNAARVVATAKDFDKVGLGIIGYYLQLYAVELILSEEDRSQEMTALATELLDTIEAFKKEIGGESEAEDSDKSLHVMNTLIHDQEKAKIYMLNFTMSLYNEKLKQLKDGPWDVMLKRSLWCCIDLFSCILHLWKENISETSTNSLQKRIKYCKIYLSKLAKGEIG 167
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains -2rkkA01 A:1-167 Vacuolar protein sorting-associated protein vta1                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..-----------....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 -Exon 1.1  PDB: A:1-167 (gaps) UniProt: 1-330 [INCOMPLETE]                                                                                                               Transcript 1
                 2rkk A  1A SMASNAARVVATAKDFDKVGLGIIGYYLQLYAVELILSEEDRSQEMTALATELLDTIEAFKKEIG-----------LHVMNTLIHDQEKAKIYMLNFTMSLYNEKLKQLKDGPWDVMLKRSLWCCIDLFSCILHLWKENISETSTNSLQKRIKYCKIYLSKLAKGEIG 167
                            |        9        19        29        39        49        59    |    -      | 79        89        99       109       119       129       139       149       159        
                            |                                                              64          76                                                                                           
                           1A                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:157
 aligned with VTA1_YEAST | Q06263 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:168
                             1                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159        
           VTA1_YEAST     - -MASNAARVVATAKDFDKVGLGIIGYYLQLYAVELILSEEDRSQEMTALATELLDTIEAFKKEIGGESEAEDSDKSLHVMNTLIHDQEKAKIYMLNFTMSLYNEKLKQLKDGPWDVMLKRSLWCCIDLFSCILHLWKENISETSTNSLQKRIKYCKIYLSKLAKGEIG 167
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains -2rkkB01 B:1-167 Vacuolar protein sorting-associated protein vta1                                                                                                        CATH domains
           Pfam domains (1) ---DUF605-2rkkB01 B:3-167                                                                                                                                                Pfam domains (1)
           Pfam domains (2) ---DUF605-2rkkB02 B:3-167                                                                                                                                                Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.-----------..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 -Exon 1.1  PDB: B:1-167 (gaps) UniProt: 1-330 [INCOMPLETE]                                                                                                               Transcript 1
                 2rkk B  1A SMASNAARVVATAKDFDKVGLGIIGYYLQLYAVELILSEEDRSQEMTALATELLDTIEAFKKEIG-----------LHVMNTLIHDQEKAKIYMLNFTMSLYNEKLKQLKDGPWDVMLKRSLWCCIDLFSCILHLWKENISETSTNSLQKRIKYCKIYLSKLAKGEIG 167
                            |        9        19        29        39        49        59    |    -      | 79        89        99       109       119       129       139       149       159        
                           1A                                                              64          76
   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 2RKK)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: DUF605] (3)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (VTA1_YEAST | Q06263)
molecular function
    GO:0001671    ATPase activator activity    Binds to and increases the ATP hydrolysis activity of an ATPase.
    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: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:0006869    lipid transport    The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0032781    positive regulation of ATPase activity    Any process that activates or increases the rate of ATP hydrolysis by an ATPase.
    GO:0032461    positive regulation of protein oligomerization    Any process that activates or increases the frequency, rate or extent of protein oligomerization.
    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.
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: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.
    GO:0005771    multivesicular body    A type of 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.

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  VTA1_YEAST | Q06263
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 Related Entries

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

UniProtKB/Swiss-Prot
        VTA1_YEAST | Q06263: 2luh 2rkl 3mhv 5h7p 5uie

(-) Related Entries Specified in the PDB File

2rkl