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(-) Description

Title :  YEAST DELTA-COP-I MU-HOMOLOGY DOMAIN COMPLEXED WITH GCS1 WXXF PEPTIDE
 
Authors :  R. J. Suckling, P. R. Evans, D. J. Owen
Date :  13 Oct 15  (Deposition) - 11 Nov 15  (Release) - 02 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,E  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  C  (1x)
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
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: MU-HOMOLOGY DOMAIN, RESIDUES 3282-546
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: DELTA-COAT PROTEIN, DELTA-COP
 
Molecule 2 - ADP-RIBOSYLATION FACTOR GTPASE-ACTIVATING PROTEIN GCS1
    Chains: D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 345-352
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: ARF GAP GCS1

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): A   E
Biological Unit 2 (1x):  B D 
Biological Unit 3 (1x):   C  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 15)

Asymmetric Unit (1, 15)
No.NameCountTypeFull Name
1MSE15Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 5FJX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FJX)

(-) 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: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..........eeeeee...eeeeeeeee....eeeeeeeee..hhhhhh.eeee.eeeee...........eeeeee..eeeee...eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fjx 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  
                                                                                                                                                                                                         460-MSE                             496-MSE            515-MSE  |                        
                                                                                                                                                                                                             464-MSE                                                   522-MSE                    


Chain B from PDB  Type:PROTEIN  Length:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeeeee.....eeeeeeeeeeeeee.......eeeee.......hhhhh.ee....hhhhhhhhhee...............eeeeeeeeee.........eeee..........ee..eeeeee.....eeeeeeee....................eeeee.....eeeeeeee....eeeee..ee..hhhhhh.eeee.eeeee...........eeeeee..........eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fjx B 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  
                                                                                                                                                                                                         460-MSE                             496-MSE            515-MSE  |                        
                                                                                                                                                                                                             464-MSE                                                   522-MSE                    


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.............ee....hhhhhhhhhee...............eeeeeeeee..........eeeeeeeee.....eeeeeeeeee.....eeeeeeee........ee..........eeeeee...eeeeeeeee....eeeeeeeee..hhhhhh.eeee.eeee............eeeeee..eeeee...eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fjx 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  
                                                                                                                                                                                                         460-MSE                             496-MSE            515-MSE  |                        
                                                                                                                                                                                                             464-MSE                                                   522-MSE                    


Chain D 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
                 5fjx D   3 DKWDDF   8


Chain E from PDB  Type:PROTEIN  Length:5
                                     
               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
                 5fjx E   4 KWDDF   8
   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 5FJX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 34)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Tyr A:494 - Pro A:495   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        COPD_YEAST | P43621: 5fjw 5fjz 5fk0

(-) Related Entries Specified in the PDB File

5fjw YEAST DELTA-COP-I MU-HOMOLOGY DOMAIN COMPLEXED WITH DSL1 WXWXSEM PEPTIDE
5fjz YEAST DELTA-COP-I MU-HOMOLOGY DOMAIN COMPLEXED WITH DSL1 WXWXV PEPTIDE
5fk0 YEAST DELTA-COP-I MU-HOMOLOGY DOMAIN