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(-) Description

Title :  XFEL STRUCTURE OF THE HUMAN DELTA OPIOID RECEPTOR IN COMPLEX WITH A BIFUNCTIONAL PEPTIDE
 
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 :  02 Dec 14  (Deposition) - 14 Jan 15  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
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, X-Ray Free-Electron Laser, Serial Femtosecond Crystallography, 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
 
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  (6, 18)

Asymmetric Unit (6, 18)
No.NameCountTypeFull Name
1DI72Mod. Amino Acid2,6-DIMETHYL-L-TYROSINE
2DI82Mod. Amino Acid(3S)-1,2,3,4-TETRAHYDROISOQUINOLINE-3-CARBOXYLIC ACID
3NA2Ligand/IonSODIUM ION
4NH22Mod. Amino AcidAMINO GROUP
5OLA7Ligand/IonOLEIC ACID
6OLC3Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
Biological Unit 1 (5, 8)
No.NameCountTypeFull Name
1DI71Mod. Amino Acid2,6-DIMETHYL-L-TYROSINE
2DI81Mod. Amino Acid(3S)-1,2,3,4-TETRAHYDROISOQUINOLINE-3-CARBOXYLIC ACID
3NA-1Ligand/IonSODIUM ION
4NH21Mod. Amino AcidAMINO GROUP
5OLA3Ligand/IonOLEIC ACID
6OLC2Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
Biological Unit 2 (5, 8)
No.NameCountTypeFull Name
1DI71Mod. Amino Acid2,6-DIMETHYL-L-TYROSINE
2DI81Mod. Amino Acid(3S)-1,2,3,4-TETRAHYDROISOQUINOLINE-3-CARBOXYLIC ACID
3NA-1Ligand/IonSODIUM ION
4NH21Mod. Amino AcidAMINO GROUP
5OLA4Ligand/IonOLEIC ACID
6OLC1Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:50BINDING SITE FOR RESIDUE OLA A 1201
02AC2SOFTWAREASP A:95 , ASN A:131 , SER A:135 , HOH A:1309BINDING SITE FOR RESIDUE NA A 1202
03AC3SOFTWARELYS A:81 , ILE A:86 , LEU A:93 , ASN A:169BINDING SITE FOR RESIDUE OLC A 1204
04AC4SOFTWAREMET A:141 , ILE A:168 , ILE A:172 , LEU A:175BINDING SITE FOR RESIDUE OLC A 1205
05AC5SOFTWARESER A:44 , PRO A:294BINDING SITE FOR RESIDUE OLA A 1206
06AC6SOFTWARESER B:44 , OLA B:1204BINDING SITE FOR RESIDUE OLA B 1201
07AC7SOFTWAREASP B:95 , ASN B:131 , SER B:135 , HOH B:1313BINDING SITE FOR RESIDUE NA B 1202
08AC8SOFTWARELEU B:48 , OLA B:1201BINDING SITE FOR RESIDUE OLA B 1204
09AC9SOFTWAREILE B:86 , PHE B:89 , TRP B:173BINDING SITE FOR RESIDUE OLC B 1205
10BC1SOFTWAREASP B:128 , TYR B:129 , MET B:132 , MET B:199 , LEU B:200 , LYS B:214 , VAL B:217 , ILE B:277 , VAL B:281 , ILE B:304 , TYR B:308 , HOH G:101BINDING SITE FOR CHAIN G OF BIFUNCTIONAL PEPTIDE
11BC2SOFTWAREASP A:128 , TYR A:129 , MET A:132 , MET A:199 , LEU A:200 , LYS A:214 , VAL A:217 , ILE A:277 , VAL A:281 , ILE A:304 , TYR A:308 , HOH H:101BINDING 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 4RWD)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RWD)

(-) 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:401
                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4rwd A 1001 ADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLGARSASSLALAIAITALYSAVCAVGLLGNVLVMFGIVRYTKMKTATNIYIFNLALADALATSTLPFQSAKYLMETWPFGELLCKAVLSIDYYNMFTSIFTLTMMSVDRYIAVCHPVKALDFRTPAKAKLINICIWVLASGVGVPIMVMAVTRPRDGAVVCMLQFPSPSWYWDTVTKICVFLFAFVVPILIITVCYGLMLLRLRSVRLLSGSKEKDRSLRRITRMVLVVVGAFVVCWAPIHIFVIVWTLVDIDRRDPLVVAALHLCIALGYANSSLNPVLYAFLDENFKRCFRQLC  333
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100     || 42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332 
                                                                                                                                  1106|                                                                                                                                                                                                                                                                                                      
                                                                                                                                     39                                                                                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:400
                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee..eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4rwd B 1001 ADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLGARSASSLALAIAITALYSAVCAVGLLGNVLVMFGIVRYTKMKTATNIYIFNLALADALATSTLPFQSAKYLMETWPFGELLCKAVLSIDYYNMFTSIFTLTMMSVDRYIAVCHPVKALDFRTPAKAKLINICIWVLASGVGVPIMVMAVTRPRDGAVVCMLQFPSPSWYWDTVTKICVFLFAFVVPILIITVCYGLMLLRLRSVRLLSGSKEKDRSLRRITRMVLVVVGAFVVCWAPIHIFVIVWTLVDIDRRDPLVVAALHLCIALGYANSSLNPVLYAFLDENFKRCFRQL  332
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100     || 42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332
                                                                                                                                  1106|                                                                                                                                                                                                                                                                                                     
                                                                                                                                     39                                                                                                                                                                                                                                                                                                     


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
                4rwd 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
                4rwd 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 4RWD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (48, 48)

Asymmetric Unit(hide GO term definitions)

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  4rwd
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  C562_ECOLX | P0ABE7
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  OPRD_HUMAN | P41143
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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 4rwa 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 4rwa

(-) Related Entries Specified in the PDB File

4ej4
4n6h
4rwa RELATED ID: GPCR-39 RELATED DB: TARGETTRACK