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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  YEAST DELTA-COP-I MU-HOMOLOGY DOMAIN COMPLEXED WITH DSL1 WXWXV PEPTIDE
 
Authors :  R. J. Suckling, P. R. Evans, D. J. Owen
Date :  14 Oct 15  (Deposition) - 11 Nov 15  (Release) - 02 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D,P,Q,R,S
Keywords :  Protein Transport, Cop-I, Vesicle Coat Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. J. Suckling, P. P. Poon, S. M. Travis, I. V. Majoul, F. M. Hughson, P. R. Evans, R. Duden, D. J. Owen
Structural Basis For The Binding Of Tryptophan-Based Motifs By Delta-Cop.
Proc. Natl. Acad. Sci. Usa V. 112 14242 2015
PubMed-ID: 26578768  |  Reference-DOI: 10.1073/PNAS.1506186112

(-) Compounds

Molecule 1 - COATOMER SUBUNIT DELTA
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: MU-HOMOLOGY DOMAIN, RESIDUES 282-546
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: DELTA-COAT PROTEIN, DELTA-COP
 
Molecule 2 - PROTEIN TRANSPORT PROTEIN DSL1
    Chains: P, Q, R, S
    Fragment: WXW MOTIF, RESIDUES 411-419
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: DEPENDENT ON SLY1-20 PROTEIN 1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDPQRS

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5FJZ)

(-) Sites  (0, 0)

(no "Site" information available for 5FJZ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FJZ)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:494 -Pro A:495
2Tyr B:494 -Pro B:495
3Tyr C:494 -Pro C:495
4Tyr D:494 -Pro D:495

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FJZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FJZ)

(-) Exons   (0, 0)

(no "Exon" information available for 5FJZ)

(-) Sequences/Alignments

Asymmetric/Biological 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:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeeeee.....eeeeeeeeeeeeee.hhhhh.eeeee.......hhhhh.ee....hhhhhhhhhee...............eeeeeeeeee.........eeeeeeeee.....eeeeeeeeee.....eeeeeeee........ee.hhhh.....eee.......eeeeeeee....eeeeeeeee..hhhhhh.eeee.eeeee...........eeeeee..........eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fjz A 285 VPENNGILISIKEVINAEFSRDGTIHSSELKGVLELRINDHDLSHSNLKLADSIDVRDKSFQFKTHPNIDKQSFLSTKLISLRDKSKAFPANDQSLGVLRWRKVAPAEDDSLIPLTLTTAVSPSESQQGFDVIIEYESVLETELADVIFTIPVFPQEPVDINTESSTCSDAEVVNMDQEMGTSIKISKIAANDAGALAFTIEAPYEDALYPMTVSFQESTRDKLAKSFTGMAIQSVVMANDHDQELPYDVITSLKSDEYLVQ 546
                                   294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544  


Chain B from PDB  Type:PROTEIN  Length:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeeeeee....eeeeeeeeeeeeee.hhhhh.eeeee.......hhhhh.ee....hhhhhhhhhee...............eeeeeeeeee.........eeeeeeee........eeeeeeee.....eeeeeeee........ee........eee.......eeeeeeee....eeeeeee....hhhhhh.eeee.eeeee...........eeeeee..........eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fjz B 285 VPENNGILISIKEVINAEFSRDGTIHSSELKGVLELRINDHDLSHSNLKLADSIDVRDKSFQFKTHPNIDKQSFLSTKLISLRDKSKAFPANDQSLGVLRWRKVAPAEDDSLIPLTLTTAVSPSESQQGFDVIIEYESVLETELADVIFTIPVFPQEPVDINTESSSDAEVVNMDQEMGTSIKISKIAANDAGALAFTIEAPYEDALYPMTVSFQESTRDKLAKSFTGMAIQSVVMANDHDQELPYDVITSLKSDEYLVQ 546
                                   294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444     ||456       466       476       486       496       506       516       526       536       546
                                                                                                                                                                                               450|                                                                                             
                                                                                                                                                                                                453                                                                                             


Chain C from PDB  Type:PROTEIN  Length:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeeeee.....eeeeeeeeeeeeee.hhhhh.eeeee.......hhhhh.ee....hhhhhhhhhee...............eeeeeeeeee.........eeeeeeeee.....eeeeeeeeee.....eeeeeeee........ee.hhhh.....eee.......eeeeeeee....eeeeeeeee..hhhhhh.eeee.eeeee...........eeeeee..eeeee...eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fjz C 285 VPENNGILISIKEVINAEFSRDGTIHSSELKGVLELRINDHDLSHSNLKLADSIDVRDKSFQFKTHPNIDKQSFLSTKLISLRDKSKAFPANDQSLGVLRWRKVAPAEDDSLIPLTLTTAVSPSESQQGFDVIIEYESVLETELADVIFTIPVFPQEPVDINTESSTCSDAEVVNMDQEMGTSIKISKIAANDAGALAFTIEAPYEDALYPMTVSFQESTRDKLAKSFTGMAIQSVVMANDHDQELPYDVITSLKSDEYLVQ 546
                                   294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544  


Chain D from PDB  Type:PROTEIN  Length:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeeeee.....eeeeeeeeeeeeee.hhhhh.eeeee.......hhhhh.ee....hhhhhhhhhee...............eeeeeeeeee.........eeeeeeeee......eeeeeeeee.....eeeeeeee........ee.........eeee.......eeeeeeee....eeeeeeee...hhhhhh.eeee.eeeee...........eeeeee..........eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fjz D 285 VPENNGILISIKEVINAEFSRDGTIHSSELKGVLELRINDHDLSHSNLKLADSIDVRDKSFQFKTHPNIDKQSFLSTKLISLRDKSKAFPANDQSLGVLRWRKVAPAEDDSLIPLTLTTAVSPSESQQGFDVIIEYESVLETELADVIFTIPVFPQEPVDINTESSTCSDAEVVNMDQEMGTSIKISKIAANDAGALAFTIEAPYEDALYPMTVSFQESTRDKLAKSFTGMAIQSVVMANDHDQELPYDVITSLKSDEYLVQ 546
                                   294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544  


Chain P from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 5fjz P   2 DWNWEV   7


Chain Q from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 5fjz Q   2 DWNWEV   7


Chain R from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 5fjz R   2 DWNWEV   7


Chain S from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 5fjz S   2 DWNWEV   7
   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  (0, 0)

(no "SCOP Domain" information available for 5FJZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FJZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FJZ)

(-) Gene Ontology  (22, 29)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Tyr A:494 - Pro A:495   [ RasMol ]  
    Tyr B:494 - Pro B:495   [ RasMol ]  
    Tyr C:494 - Pro C:495   [ RasMol ]  
    Tyr D:494 - Pro D:495   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        COPD_YEAST | P43621: 5fjw 5fjx 5fk0
        DSL1_YEAST | P53847: 3etu 3etv 5fjw

(-) Related Entries Specified in the PDB File

5fjw YEAST DELTA-COP-I MU-HOMOLOGY DOMAIN COMPLEXED WITH DSL1 WXWXSEM PEPTIDE
5fjx YEAST DELTA-COP-I MU-HOMOLOGY DOMAIN COMPLEXED WITH GCS1 WXXF PEPTIDE
5fk0 YEAST DELTA-COP-I MU-HOMOLOGY DOMAIN