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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF VPS28
 
Authors :  E. Pineda-Molina, H. Belrhali, A. J. Piefer, I. Akula, P. Bates, W. Weis
Date :  20 Feb 06  (Deposition) - 27 Jun 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.05
Chains :  Asym. Unit :  A,B,C,D,E,F,G
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Biol. Unit 7:  G  (1x)
Biol. Unit 8:  A,B  (1x)
Biol. Unit 9:  A,B,F  (1x)
Biol. Unit 10:  C (1x),G (1x)
Biol. Unit 11:  A,F  (1x)
Keywords :  4 Helix Bundle, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Pineda-Molina, H. Belrhali, A. J. Piefer, I. Akula, P. Bates, W. Weissenhorn
The Crystal Structure Of The C-Terminal Domain Of Vps28 Reveals A Conserved Surface Required For Vps20 Recruitment.
Traffic V. 7 1007 2006
PubMed-ID: 16749904  |  Reference-DOI: 10.1111/J.1600-0854.2006.00440.X

(-) Compounds

Molecule 1 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VPS28
    ChainsA, B, C, D, E, F, G
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21 (DE3) CODON PLUS
    Expression System Taxid562
    Expression System VectorPPROEX-HTA
    Expression System Vector TypePLASMID
    GeneVPS28
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit ABCDEFG
Biological Unit 1 (1x)A      
Biological Unit 2 (1x) B     
Biological Unit 3 (1x)  C    
Biological Unit 4 (1x)   D   
Biological Unit 5 (1x)    E  
Biological Unit 6 (1x)     F 
Biological Unit 7 (1x)      G
Biological Unit 8 (1x)AB     
Biological Unit 9 (1x)AB   F 
Biological Unit 10 (1x)  C (1x)   G (1x)
Biological Unit 11 (1x)A    F 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 7 (1, 1)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 8 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 9 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 10 (1, 1)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 11 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2G3K)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2G3K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2G3K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2G3K)

(-) PROSITE Motifs  (1, 7)

Asymmetric Unit (1, 7)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VPS28_CPS51310 VPS28 C-terminal domain profile.VPS28_YEAST148-242
 
 
 
 
 
 
  7A:148-241
B:148-241
C:148-241
D:148-241
E:148-241
F:148-241
G:148-241
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VPS28_CPS51310 VPS28 C-terminal domain profile.VPS28_YEAST148-242
 
 
 
 
 
 
  1A:148-241
-
-
-
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VPS28_CPS51310 VPS28 C-terminal domain profile.VPS28_YEAST148-242
 
 
 
 
 
 
  1-
B:148-241
-
-
-
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VPS28_CPS51310 VPS28 C-terminal domain profile.VPS28_YEAST148-242
 
 
 
 
 
 
  1-
-
C:148-241
-
-
-
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VPS28_CPS51310 VPS28 C-terminal domain profile.VPS28_YEAST148-242
 
 
 
 
 
 
  1-
-
-
D:148-241
-
-
-
Biological Unit 5 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VPS28_CPS51310 VPS28 C-terminal domain profile.VPS28_YEAST148-242
 
 
 
 
 
 
  1-
-
-
-
E:148-241
-
-
Biological Unit 6 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VPS28_CPS51310 VPS28 C-terminal domain profile.VPS28_YEAST148-242
 
 
 
 
 
 
  1-
-
-
-
-
F:148-241
-
Biological Unit 7 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VPS28_CPS51310 VPS28 C-terminal domain profile.VPS28_YEAST148-242
 
 
 
 
 
 
  1-
-
-
-
-
-
G:148-241
Biological Unit 8 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VPS28_CPS51310 VPS28 C-terminal domain profile.VPS28_YEAST148-242
 
 
 
 
 
 
  2A:148-241
B:148-241
-
-
-
-
-
Biological Unit 9 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VPS28_CPS51310 VPS28 C-terminal domain profile.VPS28_YEAST148-242
 
 
 
 
 
 
  3A:148-241
B:148-241
-
-
-
F:148-241
-
Biological Unit 10 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VPS28_CPS51310 VPS28 C-terminal domain profile.VPS28_YEAST148-242
 
 
 
 
 
 
  2-
-
C:148-241
-
-
-
G:148-241
Biological Unit 11 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VPS28_CPS51310 VPS28 C-terminal domain profile.VPS28_YEAST148-242
 
 
 
 
 
 
  2A:148-241
-
-
-
-
F:148-241
-

(-) Exons   (1, 7)

Asymmetric Unit (1, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPL065W1YPL065W.1XVI:427924-428652729VPS28_YEAST1-2422427A:148-241
B:148-241
C:148-241
D:148-241
E:148-241
F:148-241
G:148-241
94
94
94
94
94
94
94

(-) Sequences/Alignments

Asymmetric 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:94
 aligned with VPS28_YEAST | Q02767 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:94
                                   157       167       177       187       197       207       217       227       237    
          VPS28_YEAST   148 FNAKYVAEATGNFITVMDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWIVRINKLSIGDTLTETQIRELLFDLELAYKSFYALL 241
               SCOP domains d2g3ka1 A:148-241 Vacuolar protein sorting-associated protein 28, VPS28                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE VPS28_C  PDB: A:148-241 UniProt: 148-242                                                       PROSITE
               Transcript 1 Exon 1.1  PDB: A:148-241 UniProt: 1-242 [INCOMPLETE]                                           Transcript 1
                 2g3k A 148 FNAKYVAEATGNFITVmDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWIVRINKLSIGDTLTETQIRELLFDLELAYKSFYALL 241
                                   157      |167       177       187       197       207       217       227       237    
                                          164-MSE                                                                         

Chain B from PDB  Type:PROTEIN  Length:94
 aligned with VPS28_YEAST | Q02767 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:94
                                   157       167       177       187       197       207       217       227       237    
          VPS28_YEAST   148 FNAKYVAEATGNFITVMDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWIVRINKLSIGDTLTETQIRELLFDLELAYKSFYALL 241
               SCOP domains d2g3kb_ B: Vacuolar protein sorting-associated protein 28, VPS28                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE VPS28_C  PDB: B:148-241 UniProt: 148-242                                                       PROSITE
               Transcript 1 Exon 1.1  PDB: B:148-241 UniProt: 1-242 [INCOMPLETE]                                           Transcript 1
                 2g3k B 148 FNAKYVAEATGNFITVmDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWIVRINKLSIGDTLTETQIRELLFDLELAYKSFYALL 241
                                   157      |167       177       187       197       207       217       227       237    
                                          164-MSE                                                                         

Chain C from PDB  Type:PROTEIN  Length:94
 aligned with VPS28_YEAST | Q02767 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:94
                                   157       167       177       187       197       207       217       227       237    
          VPS28_YEAST   148 FNAKYVAEATGNFITVMDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWIVRINKLSIGDTLTETQIRELLFDLELAYKSFYALL 241
               SCOP domains d2g3kc_ C: Vacuolar protein sorting-associated protein 28, VPS28                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE VPS28_C  PDB: C:148-241 UniProt: 148-242                                                       PROSITE
               Transcript 1 Exon 1.1  PDB: C:148-241 UniProt: 1-242 [INCOMPLETE]                                           Transcript 1
                 2g3k C 148 FNAKYVAEATGNFITVmDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWIVRINKLSIGDTLTETQIRELLFDLELAYKSFYALL 241
                                   157      |167       177       187       197       207       217       227       237    
                                          164-MSE                                                                         

Chain D from PDB  Type:PROTEIN  Length:94
 aligned with VPS28_YEAST | Q02767 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:94
                                   157       167       177       187       197       207       217       227       237    
          VPS28_YEAST   148 FNAKYVAEATGNFITVMDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWIVRINKLSIGDTLTETQIRELLFDLELAYKSFYALL 241
               SCOP domains d2g3kd_ D: Vacuolar protein sorting-associated protein 28, VPS28                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE VPS28_C  PDB: D:148-241 UniProt: 148-242                                                       PROSITE
               Transcript 1 Exon 1.1  PDB: D:148-241 UniProt: 1-242 [INCOMPLETE]                                           Transcript 1
                 2g3k D 148 FNAKYVAEATGNFITVmDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWIVRINKLSIGDTLTETQIRELLFDLELAYKSFYALL 241
                                   157      |167       177       187       197       207       217       227       237    
                                          164-MSE                                                                         

Chain E from PDB  Type:PROTEIN  Length:94
 aligned with VPS28_YEAST | Q02767 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:94
                                   157       167       177       187       197       207       217       227       237    
          VPS28_YEAST   148 FNAKYVAEATGNFITVMDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWIVRINKLSIGDTLTETQIRELLFDLELAYKSFYALL 241
               SCOP domains d2g3ke_ E: Vacuolar protein sorting-associated protein 28, VPS28                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE VPS28_C  PDB: E:148-241 UniProt: 148-242                                                       PROSITE
               Transcript 1 Exon 1.1  PDB: E:148-241 UniProt: 1-242 [INCOMPLETE]                                           Transcript 1
                 2g3k E 148 FNAKYVAEATGNFITVmDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWIVRINKLSIGDTLTETQIRELLFDLELAYKSFYALL 241
                                   157      |167       177       187       197       207       217       227       237    
                                          164-MSE                                                                         

Chain F from PDB  Type:PROTEIN  Length:94
 aligned with VPS28_YEAST | Q02767 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:94
                                   157       167       177       187       197       207       217       227       237    
          VPS28_YEAST   148 FNAKYVAEATGNFITVMDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWIVRINKLSIGDTLTETQIRELLFDLELAYKSFYALL 241
               SCOP domains d2g3kf_ F: Vacuolar protein sorting-associated protein 28, VPS28                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE VPS28_C  PDB: F:148-241 UniProt: 148-242                                                       PROSITE
               Transcript 1 Exon 1.1  PDB: F:148-241 UniProt: 1-242 [INCOMPLETE]                                           Transcript 1
                 2g3k F 148 FNAKYVAEATGNFITVmDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWIVRINKLSIGDTLTETQIRELLFDLELAYKSFYALL 241
                                   157      |167       177       187       197       207       217       227       237    
                                          164-MSE                                                                         

Chain G from PDB  Type:PROTEIN  Length:94
 aligned with VPS28_YEAST | Q02767 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:94
                                   157       167       177       187       197       207       217       227       237    
          VPS28_YEAST   148 FNAKYVAEATGNFITVMDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWIVRINKLSIGDTLTETQIRELLFDLELAYKSFYALL 241
               SCOP domains d2g3kg_ G: Vacuolar protein sorting-associated protein 28, VPS28                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE VPS28_C  PDB: G:148-241 UniProt: 148-242                                                       PROSITE
               Transcript 1 Exon 1.1  PDB: G:148-241 UniProt: 1-242 [INCOMPLETE]                                           Transcript 1
                 2g3k G 148 FNAKYVAEATGNFITVmDALKLNYNAKDQLHPLLAELLISINRVTRDDFENRSKLIDWIVRINKLSIGDTLTETQIRELLFDLELAYKSFYALL 241
                                   157      |167       177       187       197       207       217       227       237    
                                          164-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, 7)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2G3K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2G3K)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G   (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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  VPS28_YEAST | Q02767
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