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(-) Description

Title :  STRUCTURE OF THE ESCRT-I ENDOSOMAL TRAFFICKING COMPLEX
 
Authors :  M. S. Kostelansky, S. Lee, J. Kim, J. H. Hurley
Date :  28 Nov 05  (Deposition) - 18 Apr 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Biol. Unit 3:  A,B,C,D,E,F  (1x)
Keywords :  Endosome, Trafficking Complex, Vps23, Vps28, Vps37, Vacuolar 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
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUPPRESSOR PROTEIN STP22 OF TEMPERATURE- SENSITIVE ALPHA-FACTOR RECEPTOR AND ARGININE PERMEASE
    Chains: A, 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: 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, E
    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 (13-125)
    Gene: VPS28, VPT28
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
 
Molecule 3 - PROTEIN SRN2
    Chains: C, F
    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: VPS37C-TERMINAL DOMAIN (132-213)
    Gene: SRN2, VPS37
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF
Biological Unit 3 (1x): ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS C:196 , ARG C:199 , THR E:107 , ALA E:108 , SER E:109BINDING SITE FOR RESIDUE SO4 C 101
2AC2SOFTWARETHR B:107 , ALA B:108 , SER B:109 , HIS F:196 , ARG F:199BINDING SITE FOR RESIDUE SO4 B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F66)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2F66)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F66)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SBPS51312 Steadiness box (SB) domain profile.STP22_YEAST322-385
 		  2A:322-385
D:322-385
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-
D:322-385
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SBPS51312 Steadiness box (SB) domain profile.STP22_YEAST322-385
 		  2A:322-385
D:322-385

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YCL008C1YCL008C.1III:106853-1056961158STP22_YEAST1-3853852A:321-385
D:321-385		65
65
2.1YLR119W1YLR119W.1XII:385535-386176642SRN2_YEAST1-2132132C:142-206
F:145-207		65
63
3.1YPL065W1YPL065W.1XVI:427924-428652729VPS28_YEAST1-2422422B:15-125
E:15-125		111
111

(-) 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 -d2f66a1 A:322-385                                                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: A:322-385 UniProt: 322-385                              PROSITE
               Transcript 1 Exon 1.1  PDB: A:321-385 UniProt: 1-385 [INCOMPLETE]              Transcript 1
                 2f66 A 321 MTDGLNQLYNLVAQDYALTDTIEALSRMLHRGTIPLDTFVKQGRELARQQFLVRWHIQRITSPLS 385
                                   330       340       350       360       370       380     


Chain B from PDB  Type:PROTEIN  Length:111
 aligned with VPS28_YEAST | Q02767 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:111
                                    24        34        44        54        64        74        84        94       104       114       124 
          VPS28_YEAST    15 SQLFHDEVPLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTNTVDKLLKQFKVYLNSQNKEEINKHFQSIEAFCDTYNITASNAITRLERGIPITAEH 125
               SCOP domains d2f66b1 B:15-125 Vacuolar protein sorting-associated protein 28, VPS28                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 3 Exon 3.1  PDB: B:15-125 UniProt: 1-242 [INCOMPLETE]                                                             Transcript 3
                 2f66 B  15 SQLFHDEVPLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTNTVDKLLKQFKVYLNSQNKEEINKHFQSIEAFADTYNITASNAITRLERGIPITAEH 125
                                    24        34        44        54        64        74        84        94       104       114       124 


Chain C from PDB  Type:PROTEIN  Length:65
 aligned with SRN2_YEAST | Q99176 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:65
                                   151       161       171       181       191       201     
           SRN2_YEAST   142 SKKYGDIALKKKLEQNTKKLDEESSQLETTTRSIDSADDLDQFIKNYLDIRTQYHLRREKLATWD 206
               SCOP domains d2f66c1 C:142-206                                                 SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: C:142-206 UniProt: 1-213 [INCOMPLETE]              Transcript 2
                 2f66 C 142 SKKYGDIALKKKLEQNTKKLDEESSQLETTTRSIDSADDLDQFIKNYLDIRTQYHLRREKLATWD 206
                                   151       161       171       181       191       201     


Chain D 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 d2f66d_ D: Vacuolar protein sorting-associated protein 23, VPS23  SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SB  PDB: D:322-385 UniProt: 322-385                              PROSITE
               Transcript 1 Exon 1.1  PDB: D:321-385 UniProt: 1-385 [INCOMPLETE]              Transcript 1
                 2f66 D 321 MTDGLNQLYNLVAQDYALTDTIEALSRMLHRGTIPLDTFVKQGRELARQQFLVRWHIQRITSPLS 385
                                   330       340       350       360       370       380     


Chain E from PDB  Type:PROTEIN  Length:111
 aligned with VPS28_YEAST | Q02767 from UniProtKB/Swiss-Prot  Length:242

    Alignment length:111
                                    24        34        44        54        64        74        84        94       104       114       124 
          VPS28_YEAST    15 SQLFHDEVPLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTNTVDKLLKQFKVYLNSQNKEEINKHFQSIEAFCDTYNITASNAITRLERGIPITAEH 125
               SCOP domains d2f66e_ E: Vacuolar protein sorting-associated protein 28, VPS28                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.....hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 3 Exon 3.1  PDB: E:15-125 UniProt: 1-242 [INCOMPLETE]                                                             Transcript 3
                 2f66 E  15 SQLFHDEVPLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTNTVDKLLKQFKVYLNSQNKEEINKHFQSIEAFADTYNITASNAITRLERGIPITAEH 125
                                    24        34        44        54        64        74        84        94       104       114       124 


Chain F from PDB  Type:PROTEIN  Length:63
 aligned with SRN2_YEAST | Q99176 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:63
                                   154       164       174       184       194       204   
           SRN2_YEAST   145 YGDIALKKKLEQNTKKLDEESSQLETTTRSIDSADDLDQFIKNYLDIRTQYHLRREKLATWDK 207
               SCOP domains d2f66f_ F:                                                      SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: F:145-207 UniProt: 1-213 [INCOMPLETE]            Transcript 2
                 2f66 F 145 YGDIALKKKLEQNTKKLDEESSQLETTTRSIDSADDLDQFIKNYLDIRTQYHLRREKLATWDK 207
                                   154       164       174       184       194       204
   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  (3, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2F66)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F66)

(-) Gene Ontology  (18, 40)

Asymmetric Unit(hide GO term definitions)
Chain A,D   (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,E   (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.

Chain C,F   (SRN2_YEAST | Q99176)
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).
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: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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  2f66
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  SRN2_YEAST | Q99176
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  STP22_YEAST | P25604
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  VPS28_YEAST | Q02767
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  SRN2_YEAST | Q99176
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  STP22_YEAST | P25604
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  VPS28_YEAST | Q02767
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SRN2_YEAST | Q99176: 2caz 2p22
        STP22_YEAST | P25604: 1uzx 2caz 2f6m 2p22 3r3q 3r42
        VPS28_YEAST | Q02767: 2caz 2f6m 2g3k 2j9u 2j9v 2p22

(-) Related Entries Specified in the PDB File

1u5t 1uzx 1w7p 1xb4