9L60 | pdb_00009l60

Gi-bound kappa opioid receptor in complex with dynorphin and positive allosteric modulator MPAM-15

• PDB DOI: https://doi.org/10.2210/pdb9L60/pdb
• EM Map EMD-62849: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Rattus norvegicus, Bos taurus
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2024-12-23 Released: 2025-12-31 
• Deposition Author(s): Zhuang, Y., Wang, Y., Xu, Y., Luo, P., Xu, H.E.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China), Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure-based design of an opioid receptor modulator for enhanced morphine analgesia

Wang, Y., Xu, Y., Xu, H.E., Zhuang, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 134.94 kDa 
• Atom Count: 7,260 
• Modeled Residue Count: 910 
• Deposited Residue Count: 1,188 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	354	Homo sapiens	Mutation(s): 2  Gene Names: GNAI1 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096  Go to UniProtKB:  P63096
PHAROS:  P63096 GTEx:  ENSG00000127955

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	353	Rattus norvegicus	Mutation(s): 0  Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus) Explore P54311  Go to UniProtKB:  P54311

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	71	Bos taurus	Mutation(s): 0  Gene Names: GNG2
UniProt
Find proteins for P63212 (Bos taurus) Explore P63212  Go to UniProtKB:  P63212

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Kappa-type opioid receptor	D	397	Homo sapiens	Mutation(s): 0  Gene Names: OPRK1, OPRK
UniProt & NIH Common Fund Data Resources
Find proteins for P41145 (Homo sapiens) Explore P41145  Go to UniProtKB:  P41145
PHAROS:  P41145 GTEx:  ENSG00000082556

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynorphin A(1-13)	E [auth P]	13	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01213 (Homo sapiens) Explore P01213  Go to UniProtKB:  P01213
PHAROS:  P01213 GTEx:  ENSG00000101327

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D6C (Subject of Investigation/LOI)	H [auth D]	9-[5-(3-chlorophenyl)furan-2-yl]-3,3,6,6-tetramethyl-4,5,7,9-tetrahydro-2~{H}-xanthene-1,8-dione C27 H27 Cl O4 ZEPFMYCUUQVNAO-UHFFFAOYSA-N
CLR (Subject of Investigation/LOI)	F [auth D], G [auth D]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-31 
Deposition Author(s): Zhuang, Y., Wang, Y., Xu, Y., Luo, P., Xu, H.E.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32130022 and 82121005
Ministry of Science and Technology (MoST, China)	China	2019YFA0904200, 2022YFC2703105 and 2022YFA1302900
Chinese Academy of Sciences	China	XDB37030103

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release