4RWD

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

• PDB DOI: https://doi.org/10.2210/pdb4RWD/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli, Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2014-12-02 Released: 2015-01-14 
• Deposition Author(s): 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.H., 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., GPCR Network (GPCR)

---

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 

Starting Models: experimental

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

• PubMed: 25686086 
• DOI: https://doi.org/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 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 95.69 kDa 
• Atom Count: 6,326 
• Modelled Residue Count: 811 
• Deposited Residue Count: 832 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,Delta-type opioid receptor	A, B	411	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 3  Gene Names: cybC, OPRD, OPRD1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P41143 (Homo sapiens) Explore P41143  Go to UniProtKB:  P41143
PHAROS:  P41143 GTEx:  ENSG00000116329
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
UniProt Groups	P0ABE7P41143

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
bifunctional peptide	C [auth G], D [auth H]	5	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLC	H [auth A], I [auth A], O [auth B]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLA	E [auth A], G [auth A], J [auth A], K [auth B], M [auth B], N [auth B], P [auth B]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
NA	F [auth A], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DI7	C [auth G], D [auth H]	L-PEPTIDE LINKING	C11 H15 N O3		TYR

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001256	C [auth G], D [auth H]	bifunctional peptide	Peptide-like / Unknown

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
• Diffraction Data: https://doi.org/10.11577/1255980

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.23	α = 90
b = 89.29	β = 92.3
c = 96.42	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): 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.H., 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., GPCR Network (GPCR)

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
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2023-09-20
  Changes: Refinement description
• Version 1.6: 2023-12-06
  Changes: Data collection, Derived calculations