8YWF | pdb_00008ywf

Cryo-EM structure of GLP1 complex bound with Retatrutide

• PDB DOI: https://doi.org/10.2210/pdb8YWF/pdb
• EM Map EMD-39631: EMDB EMDataResource

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


• Deposited: 2024-03-31 Released: 2025-04-16 
• Deposition Author(s): Zhao, L., Xu, H.E., Yuan, Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.74 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of GLP1 complex bound with Retatrutide

Zhao, L., Xu, H.E., Yuan, Q.

To be published.

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: 162.51 kDa 
• Atom Count: 9,499 
• Modeled Residue Count: 1,185 
• Deposited Residue Count: 1,434 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	A	361	Homo sapiens	Mutation(s): 0  Gene Names: GNAI1, GNAS, GNAS1, GSP EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens) Explore P63092  Go to UniProtKB:  P63092
PHAROS:  P63092 GTEx:  ENSG00000087460
Find proteins for P63096 (Homo sapiens) Explore P63096  Go to UniProtKB:  P63096
PHAROS:  P63096 GTEx:  ENSG00000127955
UniProt Groups	P63096P63092

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	397	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
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
NB35	D [auth N]	132	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Retatrutide	E [auth P]	33	Homo sapiens	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucagon-like peptide 1 receptor	F [auth R]	440	Homo sapiens	Mutation(s): 0  Gene Names: GLP1R
UniProt & NIH Common Fund Data Resources
Find proteins for P43220 (Homo sapiens) Explore P43220  Go to UniProtKB:  P43220
PHAROS:  P43220 GTEx:  ENSG00000112164

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D7Q (Subject of Investigation/LOI)	G [auth R]	20-[[(2~{S})-1-oxidanyl-1,5-bis(oxidanylidene)-5-[2-[2-(2-oxidanylideneethoxy)ethoxy]ethylamino]pentan-2-yl]amino]-20-oxidanylidene-icosanoic acid C31 H56 N2 O10 MOHNQANMYICFPX-SANMLTNESA-N

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.74 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Zhao, L., Xu, H.E., Yuan, Q.

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

Revision History  

• Version 1.0: 2025-04-16
  Type: Initial release