7Y1F | pdb_00007y1f

Cryo-EM structure of human k-opioid receptor-Gi complex

• PDB DOI: https://doi.org/10.2210/pdb7Y1F/pdb
• EM Map EMD-33562: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTM


• Deposited: 2022-06-08 Released: 2023-05-24 
• Deposition Author(s): Chen, B.O., Xu, F.E.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of human kappa-opioid receptor-Gi complex bound to an endogenous agonist dynorphin A.

Chen, Y., Chen, B., Wu, T., Zhou, F., Xu, F.

(2023) Protein Cell 14: 464-468

• PubMed: 37285260 
• DOI: https://doi.org/10.1093/procel/pwac033
• Primary Citation Related Structures: 
  7Y1F

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Organizational Affiliation: 
• iHuman Institute, ShanghaiTech University, Shanghai 210210, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai 210210, China.
Center for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
University of Chinese Academy of Sciences, Beijing 100049, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 172.66 kDa 
• Atom Count: 8,691 
• Modeled Residue Count: 1,131 
• Deposited Residue Count: 1,545 
• Unique protein chains: 6

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): 0  Gene Names: GNAI1 EC: 3.6.5 Membrane Entity: Yes
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
Dynorphin	B [auth F]	13	Homo sapiens	Mutation(s): 0  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P01213 (Homo sapiens) Explore P01213  Go to UniProtKB:  P01213
PHAROS:  P01213 GTEx:  ENSG00000101327

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Kappa-type opioid receptor	C [auth R]	460	Homo sapiens	Mutation(s): 0  Gene Names: OPRK1, OPRK Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P41145 (Homo sapiens) Explore P41145  Go to UniProtKB:  P41145
PHAROS:  P41145 GTEx:  ENSG00000082556

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	D [auth B]	351	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	E [auth C]	68	Homo sapiens	Mutation(s): 0  Gene Names: GNG2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768  Go to UniProtKB:  P59768
PHAROS:  P59768 GTEx:  ENSG00000186469

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	F [auth E]	299	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-24 
Deposition Author(s): Chen, B.O., Xu, F.E.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2023-05-24
  Type: Initial release
  
• Version 1.1: 2023-06-21
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Data collection, Structure summary
• Version 1.3: 2025-07-02
  Changes: Data collection