4RWD

XFEL structure of the human delta opioid receptor in complex with a bifunctional peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for bifunctional peptide recognition at human delta-opioid receptor.

Fenalti, G.Zatsepin, N.A.Betti, C.Giguere, P.Han, G.W.Ishchenko, A.Liu, W.Guillemyn, K.Zhang, H.James, D.Wang, D.Weierstall, U.Spence, J.C.Boutet, S.Messerschmidt, M.Williams, G.J.Gati, C.Yefanov, O.M.White, T.A.Oberthuer, D.Metz, M.Yoon, C.H.Barty, A.Chapman, H.N.Basu, S.Coe, J.Conrad, C.E.Fromme, R.Fromme, P.Tourwe, D.Schiller, P.W.Roth, B.L.Ballet, S.Katritch, V.Stevens, R.C.Cherezov, V.

(2015) Nat Struct Mol Biol 22: 265-268

  • DOI: 10.1038/nsmb.2965
  • Primary Citation of Related Structures:  
    4RWA, 4RWD

  • PubMed Abstract: 
  • Bifunctional μ- and δ-opioid receptor (OR) ligands are potential therapeutic alternatives, with diminished side effects, to alkaloid opiate analgesics. We solved the structure of human δ-OR bound to the bifunctional δ-OR antagonist and μ-OR agonist t ...

    Bifunctional μ- and δ-opioid receptor (OR) ligands are potential therapeutic alternatives, with diminished side effects, to alkaloid opiate analgesics. We solved the structure of human δ-OR bound to the bifunctional δ-OR antagonist and μ-OR agonist tetrapeptide H-Dmt-Tic-Phe-Phe-NH2 (DIPP-NH2) by serial femtosecond crystallography, revealing a cis-peptide bond between H-Dmt and Tic. The observed receptor-peptide interactions are critical for understanding of the pharmacological profiles of opioid peptides and for development of improved analgesics.


    Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Soluble cytochrome b562,Delta-type opioid receptorAB411Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 3 
Gene Names: cybC
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs): Class A
Protein: 
δ-opioid receptor with bound antagonist/agonist tetrapeptide DIPP-NH2
Find proteins for P41143 (Homo sapiens)
Explore P41143 
Go to UniProtKB:  P41143
NIH Common Fund Data Resources
PHAROS  P41143
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
bifunctional peptideGH5synthetic constructMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download CCD File 
A, B
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
OLA
Query on OLA

Download CCD File 
A, B
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DI7
Query on DI7
G,HL-PEPTIDE LINKINGC11 H15 N O3TYR
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001256
Query on PRD_001256
G, Hbifunctional peptidePeptide-like /  Unknown

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.23α = 90
b = 89.29β = 92.3
c = 96.42γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-04-01
    Changes: Database references
  • Version 1.2: 2017-06-07
    Changes: Database references, Structure summary
  • Version 1.3: 2018-02-14
    Changes: Data collection