8YW4 | pdb_00008yw4

Cryo-EM structure of the retatrutide-bound human GIPR-Gs complex

• PDB DOI: https://doi.org/10.2210/pdb8YW4/pdb
• EM Map EMD-39622: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMmpstruc


• Deposited: 2024-03-29 Released: 2024-09-18 
• Deposition Author(s): Li, W.Z., Zhou, Q.T., Cong, Z.T., Yuan, Q.N., Li, W.X., Zhao, F.H., Xu, H.E., Zhao, L.H., Yang, D.H., Wang, M.W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.26 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into the triple agonism at GLP-1R, GIPR and GCGR manifested by retatrutide.

Li, W., Zhou, Q., Cong, Z., Yuan, Q., Li, W., Zhao, F., Xu, H.E., Zhao, L.H., Yang, D., Wang, M.W.

(2024) Cell Discov 10: 77-77

• PubMed: 39019866 
• DOI: https://doi.org/10.1038/s41421-024-00700-0
• Primary Citation of Related Structures:  
  8YW3, 8YW4, 8YW5

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Organizational Affiliation: 
• State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
University of Chinese Academy of Sciences, Beijing, China.
Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
Research Center for Deepsea Bioresources, Sanya, Hainan, China. [e-mail].
Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai, China. [e-mail].
Research Center for Deepsea Bioresources, Sanya, Hainan, China. [e-mail].
Department of Chemistry, School of Science, The University of Tokyo, Tokyo, Japan. [e-mail].
Engineering Research Center of Tropical Medicine Innovation and Transformation of Ministry of Education, School of Pharmacy, Hainan Medical University, Haikou, Hainan, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 170.81 kDa 
• Atom Count: 8,619 
• Modeled Residue Count: 1,082 
• Deposited Residue Count: 1,513 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mini-Gs	A	361	Homo sapiens	Mutation(s): 0  EC: 3.6.5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens) Explore P63092  Go to UniProtKB:  P63092
PHAROS:  P63092 GTEx:  ENSG00000087460

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	341	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C [auth G]	71	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody-35	D [auth N]	140	synthetic construct	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Gastric inhibitory polypeptide receptor	E [auth R]	573	Homo sapiens	Mutation(s): 0  Gene Names: GIPR Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P48546 (Homo sapiens) Explore P48546  Go to UniProtKB:  P48546
PHAROS:  P48546 GTEx:  ENSG00000010310

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
retatrutide	F [auth P]	27	Homo sapiens	Mutation(s): 0

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
2ML	F [auth P]	L-PEPTIDE LINKING	C7 H15 N O2		LEU
AIB	F [auth P]	L-PEPTIDE LINKING	C4 H9 N O2		ALA

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.26 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: 2024-09-18 
Deposition Author(s): Li, W.Z., Zhou, Q.T., Cong, Z.T., Yuan, Q.N., Li, W.X., Zhao, F.H., Xu, H.E., Zhao, L.H., Yang, D.H., Wang, M.W.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82273961
National Natural Science Foundation of China (NSFC)	China	82073904
National Natural Science Foundation of China (NSFC)	China	81872915
National Natural Science Foundation of China (NSFC)	China	82273985
National Natural Science Foundation of China (NSFC)	China	82121005
National Natural Science Foundation of China (NSFC)	China	81973373
National Natural Science Foundation of China (NSFC)	China	32200576 (Z.T.C.), 32071203(L.H.Z), 82121005(H.E.X.) and 82204474 (F.H.Z.); National Science and Technology Major

Revision History  

• Version 1.0: 2024-09-18
  Type: Initial release
  
• Version 1.1: 2024-09-25
  Changes: Data collection, Database references
• Version 1.2: 2025-07-02
  Changes: Data collection, Structure summary