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(-) Description

Title :  CRYSTAL STRUCTURE OF SUBUNIT VPS25 OF THE ENDOSOMAL TRAFFICKING COMPLEX ESCRT-II
 
Authors :  W. Weissenhorn, A. K. Wernimont
Date :  27 Aug 04  (Deposition) - 22 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Winged Helix, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Wernimont, W. Weissenhorn
Crystal Structure Of Subunit Vps25 Of The Endosomal Trafficking Complex Escrt-Ii.
Bmc Struct. Biol. V. 4 10 2004
PubMed-ID: 15579210  |  Reference-DOI: 10.1186/1472-6807-4-10
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL 23.6 KDA PROTEIN IN YUH1-URA8 INTERGENIC REGION
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YJR102C, J1957
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: VPS25

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1XB4)

(-) Sites  (0, 0)

(no "Site" information available for 1XB4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XB4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XB4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XB4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XB4)

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YJR102C1YJR102C.1X:619754-619146609VPS25_YEAST1-2022024A:1-201 (gaps)
B:1-202 (gaps)
C:3-201 (gaps)
D:2-201 (gaps)		201
202
199
200

(-) 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:180
 aligned with VPS25_YEAST | P47142 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 
          VPS25_YEAST     1 MSALPPVYSFPPLYTRQPNSLTRRQQISTWIDIISQYCKTKKIWYMSVDGTVINDNELDSGSTDNDDSKKISKNLFNNEDIQRSVSQVFIDEIWSQMTKEGKCLPIDQSGRRSSNTTTTRYFILWKSLDSWASLILQWFEDSGKLNQVITLYELSEGDETVNWEFHRMPESLLYYCLKPLCDRNRATMLKDENDKVIAIKV 201
               SCOP domains d1xb4a1 A:1-125 Vacuolar protein sorting-associated pro                 tein VPS25                                           d1xb4a2 A:126-201 Vacuolar pro  tein sorting-associated protein VPS25        SCOP domains
               CATH domains 1xb4A01 A:1-125 'Winged helix' DNA-binding domain. Chai                 n C. Domain 1                                        1xb4A02 A:126-201 'winged heli  x' repressor DNA binding domain              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eee........-----------------....ee....ee.hhhhhhhhhhhhhhh..eeee.......--....eeee...hhhhhhhhhhhhhhh.......eehhhhh--...........hhhhhhhhhhhhhhhhh.eeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-201 (gaps) UniProt: 1-202 [INCOMPLETE]                                                                                                                                                 Transcript 1
                 1xb4 A   1 MSALPPVYSFPPLYTRQPNSLTRRQQISTWIDIISQYCKTKKIWYMSVDGTVIND-----------------KNLFNNEDIQRSVSQVFIDEIWSQMTKEGKCLPIDQSGRRS--TTTTRYFILWKSLDSWASLILQWFEDSGKLNQVITLYELS--DETVNWEFHRMPESLLYYCLKPLCDRNRATMLKDENDKVIAIKV 201
                                    10        20        30        40        50    |    -         -  |     80        90       100       110  |  | 120       130       140       150    |  160       170       180       190       200 
                                                                                 55                73                                     113  |                                    155  |                                           
                                                                                                                                             116                                       158                                           


Chain B from PDB  Type:PROTEIN  Length:179
 aligned with VPS25_YEAST | P47142 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  
          VPS25_YEAST     1 MSALPPVYSFPPLYTRQPNSLTRRQQISTWIDIISQYCKTKKIWYMSVDGTVINDNELDSGSTDNDDSKKISKNLFNNEDIQRSVSQVFIDEIWSQMTKEGKCLPIDQSGRRSSNTTTTRYFILWKSLDSWASLILQWFEDSGKLNQVITLYELSEGDETVNWEFHRMPESLLYYCLKPLCDRNRATMLKDENDKVIAIKVV 202
               SCOP domains d1xb4b1 B:1-125 Vacuolar protein sorting-associated                      protein VPS25                                       d1xb4b2 B:126-202 Vacuolar prot  ein sorting-associated protein VPS25         SCOP domains
               CATH domains 1xb4B01 B:1-125 'Winged helix' DNA-binding domain. C                     hain C. Domain 1                                    1xb4B02 B:126-202 'winged helix  ' repressor DNA binding domain               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eee.....---------------------...ee....ee.hhhhhhhhhhhhhhh..eeee.............eeee...hhhhhhhhhhhhhhh.......eehhhhhh--..........hhhhhhhhhhhhhhhhh.eeee.....eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-202 (gaps) UniProt: 1-202                                                                                                                                                               Transcript 1
                 1xb4 B   1 MSALPPVYSFPPLYTRQPNSLTRRQQISTWIDIISQYCKTKKIWYMSVDGTV---------------------NLFNNEDIQRSVSQVFIDEIWSQMTKEGKCLPIDQSGRRSSNTTTTRYFILWKSLDSWASLILQWFEDSGKLNQVITLYELSE--ETVNWEFHRMPESLLYYCLKPLCDRNRATMLKDENDKVIAIKVV 202
                                    10        20        30        40        50 |       -         -   |    80        90       100       110       120       130       140       150     | 160       170       180       190       200  
                                                                              52                    74                                                                               156  |                                           
                                                                                                                                                                                        159                                           


Chain C from PDB  Type:PROTEIN  Length:180
 aligned with VPS25_YEAST | P47142 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:199
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192         
          VPS25_YEAST     3 ALPPVYSFPPLYTRQPNSLTRRQQISTWIDIISQYCKTKKIWYMSVDGTVINDNELDSGSTDNDDSKKISKNLFNNEDIQRSVSQVFIDEIWSQMTKEGKCLPIDQSGRRSSNTTTTRYFILWKSLDSWASLILQWFEDSGKLNQVITLYELSEGDETVNWEFHRMPESLLYYCLKPLCDRNRATMLKDENDKVIAIKV 201
               SCOP domains d1xb4c1 C:3-125 Vacuolar protein sorting-associated pr                otein VPS25                                          d1xb4c2 C:126-201 Vacuolar pro   tein sorting-associated protein VPS25       SCOP domains
               CATH domains 1xb4C01 C:3-125 'Winged helix' DNA-binding domain. Cha                in C. Domain 1                                       1xb4C02 C:126-201 'winged heli   x' repressor DNA binding domain             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eee....ee...----------------....ee....ee.hhhhhhhhhhhhhhh..eeee.............eeee...hhhhhhhhhhhhhhh......eee.....---..........hhhhhhhhhhhhhhhhh.eeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:3-201 (gaps) UniProt: 1-202 [INCOMPLETE]                                                                                                                                               Transcript 1
                 1xb4 C   3 ALPPVYSFPPLYTRQPNSLTRRQQISTWIDIISQYCKTKKIWYMSVDGTVINDN----------------KNLFNNEDIQRSVSQVFIDEIWSQMTKEGKCLPIDQSGRRSSNTTTTRYFILWKSLDSWASLILQWFEDSGKLNQVITLYELS---ETVNWEFHRMPESLLYYCLKPLCDRNRATMLKDENDKVIAIKV 201
                                    12        22        32        42        52   |     -         -|       82        92       102       112       122       132       142       152  |   |162       172       182       192         
                                                                                56               73                                                                               155 159                                          


Chain D from PDB  Type:PROTEIN  Length:154
 aligned with VPS25_YEAST | P47142 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:200
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201
          VPS25_YEAST     2 SALPPVYSFPPLYTRQPNSLTRRQQISTWIDIISQYCKTKKIWYMSVDGTVINDNELDSGSTDNDDSKKISKNLFNNEDIQRSVSQVFIDEIWSQMTKEGKCLPIDQSGRRSSNTTTTRYFILWKSLDSWASLILQWFEDSGKLNQVITLYELSEGDETVNWEFHRMPESLLYYCLKPLCDRNRATMLKDENDKVIAIKV 201
               SCOP domains d1xb4d1 D:2-125 V   acuolar protein sorting-associate                   d protein VPS25                                     d1xb4d2 D:126-   201 Vacuolar      protein sorting-associat  ed protein VPS2 SCOP domains
               CATH domains 1xb4D01 D:2-125 '   Winged helix' DNA-binding domain.                    Chain C. Domain 1                                  1xb4D02 D:126-   201 'winged h     elix' repressor DNA bind  ing domain      CATH domains
           Pfam domains (1) ----ESCRT-II-1xb4   D01 D:6-171                                                                                                                                           -------------  --------------- Pfam domains (1)
           Pfam domains (2) ----ESCRT-II-1xb4   D02 D:6-171                                                                                                                                           -------------  --------------- Pfam domains (2)
           Pfam domains (3) ----ESCRT-II-1xb4   D03 D:6-171                                                                                                                                           -------------  --------------- Pfam domains (3)
           Pfam domains (4) ----ESCRT-II-1xb4   D04 D:6-171                                                                                                                                           -------------  --------------- Pfam domains (4)
         Sec.struct. author ........hhhhhh...---...hhhhhhhhhhhhhhhhh.............-------------------...ee....ee.hhhhhhhhhhhhhhh..ee..--------------.ee...hhhhhhhhhhhhh---....eeee.....-----...........hhhhhhhhhhhh.--...........eeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:2-201 (gaps) UniProt: 1-202 [INCOMPLETE]                                                                                                                                                Transcript 1
                 1xb4 D   2 SALPPVYSFPPLYTRQP---TRRQQISTWIDIISQYCKTKKIWYMSVDGTVIN-------------------NLFNNEDIQRSVSQVFIDEIWSQMTKEGKCLPI--------------YFILWKSLDSWASLILQWF---GKLNQVITLYELS-----VNWEFHRMPESLLYYCLKPLCDRN--TMLKDENDKVIAIKV 201
                                    11      |  -|       31        41        51  |      -         -  |     81        91       101    |    -       121       131       | - |     151   |   161       171       181  |  | 191       201
                                           18  22                              54                  74                             106            121               139 143         155   161                    184  |              
                                                                                                                                                                                                                   187
   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, 8)

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

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: ESCRT-II] (3)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (VPS25_YEAST | P47142)
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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0000433    negative regulation of transcription from RNA polymerase II promoter by glucose    Any process involving glucose that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter.
    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:0000814    ESCRT II complex    An endosomal sorting complex required for transport and functions downstream of ESCRT I complex. It consists of the class E vacuolar protein sorting (Vps) proteins and is required for the membrane recruitment of ESCRT III complex and binds to 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: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.

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  1xb4
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 Related Entries

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UniProtKB/Swiss-Prot
        VPS25_YEAST | P47142: 1u5t 1w7p

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