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(-) Description

Title :  2 ANGSTROM X-RAY STRUCTURE OF THE YEAST ESCRT-I VPS28 C-TERMINUS
 
Authors :  D. J. Gill, H. L. Teo, J. Sun, O. Perisic, D. B. Veprintsev, S. D. Emr, R. L. Williams
Date :  16 Nov 06  (Deposition) - 23 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Nzf Finger, Hiv Budding, Protein Transport, Vps, Mvb, Chmp, Escrt, Vps36, Vps28, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Gill, H. Teo, J. Sun, O. Perisic, D. B. Veprintsev, S. D. Emr, R. L. Williams
Structural Insight Into The Escrt-I/-Ii Link And Its Role In Mvb Trafficking.
Embo J. V. 26 600 2007
PubMed-ID: 17215868  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601501

(-) Compounds

Molecule 1 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 28
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: POPC
    Expression System Strain: C41 (DE3)
    Expression System Taxid: 562
    Fragment: RESIDUES 148-242
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: VPS28

 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 2J9V)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J9V)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VPS28_CPS51310 VPS28 C-terminal domain profile.VPS28_YEAST148-242  1A:148-242

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPL065W1YPL065W.1XVI:427924-428652729VPS28_YEAST1-2422421A:144-24299

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:99
 aligned with VPS28_YEAST | Q02767 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:99
                                   153       163       173       183       193       203       213       223       233         
          VPS28_YEAST   144 SDKKFNAKYVAEATGNFITVMDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWIVRINKLSIGDTLTETQIRELLFDLELAYKSFYALLD 242
               SCOP domains d2j9va_ A: automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----VPS28_C  PDB: A:148-242 UniProt: 148-242                                                        PROSITE
               Transcript 1 Exon 1.1  PDB: A:144-242 UniProt: 1-242 [INCOMPLETE]                                                Transcript 1
                 2j9v A 144 HHHMFNAKYVAEATGNFITVMDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWIVRINKLSIGDTLTETQIRELLFDLELAYKSFYALLD 242
                                   153       163       173       183       193       203       213       223       233
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  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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2J9V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J9V)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VPS28_YEAST | Q02767)
molecular function
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006612    protein targeting to membrane    The process of directing proteins towards a membrane, usually using signals contained within the protein.
    GO:0006623    protein targeting to vacuole    The process of directing proteins towards the vacuole, usually using signals contained within the 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:0043328    protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway    The process of directing proteins towards the vacuole that contributes to protein catabolism via the multivesicular body (MVB) pathway.
    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.
cellular component
    GO:0000813    ESCRT I complex    An endosomal sorting complex required for transport. It consists of the class E vacuolar protein sorting (Vps) proteins and interacts with ubiquitinated 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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        VPS28_YEAST | Q02767: 2caz 2f66 2f6m 2g3k 2j9u 2p22

(-) Related Entries Specified in the PDB File

2caz ESCRT-I CORE
2g3k CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF VPS28
2j9u 2 ANGSTROM X-RAY STRUCTURE OF THE YEAST ESCRT-I VPS28 C-TERMINUS IN COMPLEX WITH THE NZF-N DOMAIN FROM ESCRT-II
2j9w STRUCTURAL INSIGHT INTO THE ESCRT-I-II LINK AND ITS ROLE IN MVB TRAFFICKING