9PY3 | pdb_00009py3

Unlatched-state loperamide-mu opioid receptor-Gi GDPbS complex (rebound)

• PDB DOI: https://doi.org/10.2210/pdb9PY3/pdb
• EM Map EMD-72007: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2025-08-06 Released: 2025-11-12 
• Deposition Author(s): Gati, C., Han, G.W., Khan, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Ligand efficacy is driven by conformational control of nucleotide exchange at the mu opioid receptor.

Khan, S., Han, G.W., Gati, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 159.37 kDa 
• Atom Count: 7,227 
• Modeled Residue Count: 902 
• Deposited Residue Count: 1,408 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	A [auth B]	361	Homo sapiens	Mutation(s): 0  Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens) Explore P62873  Go to UniProtKB:  P62873
PHAROS:  P62873 GTEx:  ENSG00000078369

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	B [auth C]	71	Homo sapiens	Mutation(s): 0  Gene Names: GNG2
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768  Go to UniProtKB:  P59768
PHAROS:  P59768 GTEx:  ENSG00000186469

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,Mu-type opioid receptor	C [auth R]	622	Homo sapiens	Mutation(s): 0  Gene Names: cybC, OPRM1, MOR1
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for P35372 (Homo sapiens) Explore P35372  Go to UniProtKB:  P35372
PHAROS:  P35372 GTEx:  ENSG00000112038
UniProt Groups	P0ABE7P35372

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	D [auth A]	354	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CMV (Subject of Investigation/LOI)	G [auth R]	4-[4-(4-chlorophenyl)-4-hydroxypiperidin-1-yl]-N,N-dimethyl-2,2-diphenylbutanamide C29 H33 Cl N2 O2 RDOIQAHITMMDAJ-UHFFFAOYSA-N
VSN (Subject of Investigation/LOI)	H [auth A]	5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]guanosine C10 H15 N5 O10 P2 S QJXJXBXFIOTYHB-UUOKFMHZSA-N
CLR	E [auth R], F [auth R]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	v4.3.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Gati, C., Han, G.W., Khan, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM144965
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)	United States	AT012075

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release