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(-) Description

Title :  SYNCHROTRON STRUCTURE OF THE HUMAN DELTA OPIOID RECEPTOR IN COMPLEX WITH A BIFUNCTIONAL PEPTIDE (PSI COMMUNITY TARGET)
 
Authors :  G. Fenalti, N. A. Zatsepin, C. Betti, P. Giguere, G. W. Han, A. Ishchenko K. Guillemyn, H. Zhang, D. James, D. Wang, U. Weierstall, J. C. H. Spenc S. Boutet, M. Messerschmidt, G. J. Williams, C. Gati, O. M. Yefanov, T. D. Oberthuer, M. Metz, C. H. Yoon, A. Barty, H. N. Chapman, S. Basu, J. Co C. E. Conrad, R. Fromme, P. Fromme, D. Tourwe, P. W. Schiller, B. L. Roth S. Ballet, V. Katritch, R. C. Stevens, V. Cherezov, Gpcr Network (Gp
Date :  01 Dec 14  (Deposition) - 14 Jan 15  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.28
Chains :  Asym. Unit :  A,B,G,H
Biol. Unit 1:  A,H  (1x)
Biol. Unit 2:  B,G  (1x)
Keywords :  Human Opioid Receptor, Bifunctional Peptide, Gpcr Signaling, Gpcr Network, Membrane Protein, Psi-Biology, Structural Genomics, Gpcr, Membrane, Lipidic Cubic Phase, Bril (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Fenalti, N. A. Zatsepin, C. Betti, P. Giguere, G. W. Han, A. Ishchenko, W. Liu, K. Guillemyn, H. Zhang, D. James, D. Wang, U. Weierstall, J. C. Spence, S. Boutet, M. Messerschmidt, G. J. Williams, C. Gati, O. M. Yefanov, T. A. White, D. Oberthuer, M. Metz, C. H. Yoon, A. Barty, H. N. Chapman, S. Basu, J. Coe, C. E. Conrad R. Fromme, P. Fromme, D. Tourwe, P. W. Schiller, B. L. Roth, S. Ballet, V. Katritch, R. C. Stevens, V. Cherezov
Structural Basis For Bifunctional Peptide Recognition At Human Delta-Opioid Receptor.
Nat. Struct. Mol. Biol. V. 22 265 2015
PubMed-ID: 25686086  |  Reference-DOI: 10.1038/NSMB.2965

(-) Compounds

Molecule 1 - SOLUBLE CYTOCHROME B562,DELTA-TYPE OPIOID RECEPTOR
    Chains: A, B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Plasmid: PFASTBAC
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Gene: CYBC, OPRD, OPRD1, CYBC
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI, HOMO SAPIENS
    Organism Taxid: 562, 9606
    Synonym: CYTOCHROME B-562,D-OR-1, DOR-1
 
Molecule 2 - BIFUNCTIONAL PEPTIDE
    Chains: G, H
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABGH
Biological Unit 1 (1x): A  H
Biological Unit 2 (1x):  BG 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1DI72Mod. Amino Acid2,6-DIMETHYL-L-TYROSINE
2DI82Mod. Amino Acid(3S)-1,2,3,4-TETRAHYDROISOQUINOLINE-3-CARBOXYLIC ACID
3NH22Mod. Amino AcidAMINO GROUP
4OLC1Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
1DI71Mod. Amino Acid2,6-DIMETHYL-L-TYROSINE
2DI81Mod. Amino Acid(3S)-1,2,3,4-TETRAHYDROISOQUINOLINE-3-CARBOXYLIC ACID
3NH21Mod. Amino AcidAMINO GROUP
4OLC1Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1DI71Mod. Amino Acid2,6-DIMETHYL-L-TYROSINE
2DI81Mod. Amino Acid(3S)-1,2,3,4-TETRAHYDROISOQUINOLINE-3-CARBOXYLIC ACID
3NH21Mod. Amino AcidAMINO GROUP
4OLC-1Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:137 , MET A:141 , CYS A:171 , ILE A:172 , PRO A:225BINDING SITE FOR RESIDUE OLC A 1201
2AC2SOFTWARELEU B:125 , ASP B:128 , TYR B:129 , MET B:132 , VAL B:217 , VAL B:281 , TRP B:284 , ILE B:304 , TYR B:308BINDING SITE FOR CHAIN G OF BIFUNCTIONAL PEPTIDE
3AC3SOFTWARELEU A:125 , ASP A:128 , TYR A:129 , MET A:132 , MET A:199 , LEU A:200 , VAL A:217 , ILE A:277 , VAL A:281 , ILE A:304 , TYR A:308BINDING SITE FOR CHAIN H OF BIFUNCTIONAL PEPTIDE

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:121 -A:198
2B:121 -B:198

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:204 -Pro A:205
2Ser B:204 -Pro B:205
3Di7 G:1 -Di8 G:2
4Di7 H:1 -Di8 H:2

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RWA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RWA)

(-) Exons   (0, 0)

(no "Exon" information available for 4RWA)

(-) 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:391
                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4rwa A 1002 DLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLGARSASSLALAIAITALYSAVCAVGLLGNVLVMFGIVRYTKMKTATNIYIFNLALADALATSTLPFQSAKYLMETWPFGELLCKAVLSIDYYNMFTSIFTLTMMSVDRYIAVCHPVKALDFRTPAKAKLINICIWVLASGVGVPIMVMAVTRPRDGAVVCMLQFPSPSWYWDTVTKICVFLFAFVVPILIITVCYGLMLLGSKEKDRSLRRITRMVLVVVGAFVVCWAPIHIFVIVWTLVDIDRRDPLVVAALHLCIALGYANSSLNPVLYAFLDENFKRCFRQLC  333
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091      1101    ||  43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    || 252       262       272       282       292       302       312       322       332 
                                                                                                                                 1106|                                                                                                                                                                                                    238|                                                                                     
                                                                                                                                    39                                                                                                                                                                                                     248                                                                                     


Chain B from PDB  Type:PROTEIN  Length:389
                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4rwa B 1002 DLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLGARSASSLALAIAITALYSAVCAVGLLGNVLVMFGIVRYTKMKTATNIYIFNLALADALATSTLPFQSAKYLMETWPFGELLCKAVLSIDYYNMFTSIFTLTMMSVDRYIAVCHPVKALDFRTPAKAKLINICIWVLASGVGVPIMVMAVTRPRDGAVVCMLQFPSPSWYWDTVTKICVFLFAFVVPILIITVCYGLMLLRGSKEKDRSLRRITRMVLVVVGAFVVCWAPIHIFVIVWTLVDIDRRDPLVVAALHLCIALGYANSSLNPVLYAFLDENFKRCFR  330
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091      1101    ||  43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233     ||251       261       271       281       291       301       311       321         
                                                                                                                                 1106|                                                                                                                                                                                                     239|                                                                                  
                                                                                                                                    39                                                                                                                                                                                                      248                                                                                  


Chain G 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
                4rwa G    1 yxFFx    5
                            ||  |
                            1-DI7
                             2-DI8
                                5-NH2


Chain H 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
                4rwa H    1 yxFFx    5
                            ||  |
                            ||  |
                            1-DI7
                             2-DI8
                                5-NH2
   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 4RWA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RWA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RWA)

(-) Gene Ontology  (48, 48)

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 Related Entries

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

UniProtKB/Swiss-Prot
        C562_ECOLX | P0ABE7: 1apc 1lm3 1m6t 1qpu 1qq3 256b 2bc5 2qla 3c62 3c63 3de8 3de9 3foo 3fop 3hni 3hnj 3hnk 3hnl 3iq5 3iq6 3l1m 3m15 3m4b 3m4c 3m79 3nmi 3nmj 3nmk 3tol 3tom 3u8p 4ea3 4eiy 4iaq 4iar 4ib4 4je9 4jea 4jeb 4jkv 4l6r 4n6h 4nc3 4ntj 4o9r 4or2 4pxz 4py0 4qim 4qin 4rwd 4u9d 4u9e 4yay 4z34 4z35 4z36 4zud 5awi 5bu7 5dhg 5dhh 5iu4 5iu7 5iu8 5iua 5iub 5jtb 5k2a 5k2b 5k2c 5k2d 5l31 5l32 5l7d 5l7i 5ndd 5ndz 5nj6 5tvn 5uen 5uig 5unf 5ung 5unh 5uvi
        OPRD_HUMAN | P41143: 1ozc 2iqm 4n6h 4rwd

(-) Related Entries Specified in the PDB File

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