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(-) Description

Title :  STRUCTURE OF A VPS23-C:VPS28-N SUBCOMPLEX
 
Authors :  M. S. Kostelansky, S. Lee, J. Kim, J. H. Hurley
Date :  29 Nov 05  (Deposition) - 18 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Endosomes, Trafficking Complex, Vps23, Vps28, Vacuole Protein Sorting, Escrt Protein Complexes, Endosomal Sorting Complex Required For Transport, Escrt-I, Ubiquitin, Tsg101, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. S. Kostelansky, J. Sun, S. Lee, J. Kim, R. Ghirlando, A. Hierro, S. D. Emr, J. H. Hurley
Structural And Functional Organization Of The Escrt-I Trafficking Complex.
Cell(Cambridge, Mass. ) V. 125 113 2006
PubMed-ID: 16615894  |  Reference-DOI: 10.1016/J.CELL.2006.01.049

(-) Compounds

Molecule 1 - SUPPRESSOR PROTEIN STP22 OF TEMPERATURE-SENSITIVE ALPHA- FACTOR RECEPTOR AND ARGININE PERMEASE
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PST39
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: VPS23C-TERMINAL DOMAIN (322-385)
    Gene: STP22, VPS23
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VPS23
 
Molecule 2 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VPS28
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PST39
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: VPS28N-TERMINAL DOMAIN (13-118)
    Gene: VPS28, VPT28
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1DDQ8Ligand/IonDECYLAMINE-N,N-DIMETHYL-N-OXIDE
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1DDQ5Ligand/IonDECYLAMINE-N,N-DIMETHYL-N-OXIDE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1DDQ3Ligand/IonDECYLAMINE-N,N-DIMETHYL-N-OXIDE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:340BINDING SITE FOR RESIDUE MG A 109
2AC2SOFTWARETHR A:341 , LEU A:366 , LEU C:345 , GLN C:362 , LEU C:366BINDING SITE FOR RESIDUE DDQ A 101
3AC3SOFTWARETHR A:358 , HOH C:6 , HOH C:10 , GLN C:334 , GLN C:369BINDING SITE FOR RESIDUE DDQ A 102
4AC4SOFTWARETRP A:375 , GLN A:378 , TYR B:44 , SER B:96BINDING SITE FOR RESIDUE DDQ B 119
5AC5SOFTWAREMET C:321 , ILE C:377 , THR C:381BINDING SITE FOR RESIDUE DDQ C 105
6AC6SOFTWAREASN C:326 , TYR C:329 , THR D:103BINDING SITE FOR RESIDUE DDQ D 119
7AC7SOFTWARETYR A:329 , ASP A:335 , TYR B:104BINDING SITE FOR RESIDUE DDQ B 120
8AC8SOFTWARETHR C:322 , LEU C:328 , PRO C:383 , GLN D:16BINDING SITE FOR RESIDUE DDQ C 108

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F6M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2F6M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F6M)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SBPS51312 Steadiness box (SB) domain profile.STP22_YEAST322-385
 		  2A:322-385
C:322-383
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SBPS51312 Steadiness box (SB) domain profile.STP22_YEAST322-385
 		  1A:322-385
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SBPS51312 Steadiness box (SB) domain profile.STP22_YEAST322-385
 		  1-
C:322-383

(-) Exons   (2, 4)

Asymmetric Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YCL008C1YCL008C.1III:106853-1056961158STP22_YEAST1-3853852A:321-385
C:321-383		65
63
2.1YPL065W1YPL065W.1XVI:427924-428652729VPS28_YEAST1-2422422B:12-118
D:16-117		107
102

(-) 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:65
 aligned with STP22_YEAST | P25604 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:65
                                   330       340       350       360       370       380     
          STP22_YEAST   321 KTDGLNQLYNLVAQDYALTDTIECLSRMLHRGTIPLDTFVKQGRELARQQFLVRWHIQRITSPLS 385
               SCOP domains d2f6ma_ A: Vacuolar protein sorting-associated protein 23, VPS23  SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SB  PDB: A:322-385 UniProt: 322-385                              PROSITE
               Transcript 1 Exon 1.1  PDB: A:321-385 UniProt: 1-385 [INCOMPLETE]              Transcript 1
                 2f6m A 321 MTDGLNQLYNLVAQDYALTDTIEALSRMLHRGTIPLDTFVKQGRELARQQFLVRWHIQRITSPLS 385
                                   330       340       350       360       370       380     


Chain B from PDB  Type:PROTEIN  Length:107
 aligned with VPS28_YEAST | Q02767 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:107
                                    21        31        41        51        61        71        81        91       101       111       
          VPS28_YEAST    12 QDISQLFHDEVPLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTNTVDKLLKQFKVYLNSQNKEEINKHFQSIEAFCDTYNITASNAITRLERG 118
               SCOP domains d2f6mb_ B: Vacuolar protein sorting-associated protein 28, VPS28                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: B:12-118 UniProt: 1-242 [INCOMPLETE]                                                         Transcript 2
                 2f6m B  12 MDISQLFHDEVPLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTNTVDKLLKQFKVYLNSQNKEEINKHFQSIEAFADTYNITASNAITRLERG 118
                                    21        31        41        51        61        71        81        91       101       111       


Chain C from PDB  Type:PROTEIN  Length:63
 aligned with STP22_YEAST | P25604 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:63
                                   330       340       350       360       370       380   
          STP22_YEAST   321 KTDGLNQLYNLVAQDYALTDTIECLSRMLHRGTIPLDTFVKQGRELARQQFLVRWHIQRITSP 383
               SCOP domains d2f6mc_ C:                                                      SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SB  PDB: C:322-383 UniProt: 322-385                            PROSITE
               Transcript 1 Exon 1.1  PDB: C:321-383 UniProt: 1-385 [INCOMPLETE]            Transcript 1
                 2f6m C 321 MTDGLNQLYNLVAQDYALTDTIEALSRMLHRGTIPLDTFVKQGRELARQQFLVRWHIQRITSP 383
                                   330       340       350       360       370       380   


Chain D from PDB  Type:PROTEIN  Length:102
 aligned with VPS28_YEAST | Q02767 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:102
                                    25        35        45        55        65        75        85        95       105       115  
          VPS28_YEAST    16 QLFHDEVPLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTNTVDKLLKQFKVYLNSQNKEEINKHFQSIEAFCDTYNITASNAITRLER 117
               SCOP domains d2f6md_ D: Vacuolar protein sorting-associated protein 28, VPS28                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhh...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 2 Exon 2.1  PDB: D:16-117 UniProt: 1-242 [INCOMPLETE]                                                    Transcript 2
                 2f6m D  16 QLFHDEVPLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTNTVDKLLKQFKVYLNSQNKEEINKHFQSIEAFADTYNITASNAITRLER 117
                                    25        35        45        55        65        75        85        95       105       115
   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  (2, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2F6M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F6M)

(-) Gene Ontology  (18, 29)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (STP22_YEAST | P25604)
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:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
biological process
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    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:1902915    negative regulation of protein polyubiquitination    Any process that stops, prevents or reduces the frequency, rate or extent of protein polyubiquitination.
    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: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:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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.

Chain B,D   (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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 Related Entries

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

UniProtKB/Swiss-Prot
        STP22_YEAST | P25604: 1uzx 2caz 2f66 2p22 3r3q 3r42
        VPS28_YEAST | Q02767: 2caz 2f66 2g3k 2j9u 2j9v 2p22

(-) Related Entries Specified in the PDB File

1u5t 1uzx 1w7p 1xb4 2f66