8ZRK | pdb_00008zrk

Cryo-EM structure of GPR119-Gs Complex with small molecule agonist GSK-1292263

• PDB DOI: https://doi.org/10.2210/pdb8ZRK/pdb
• EM Map EMD-60399: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-04 Released: 2024-06-19 
• Deposition Author(s): Wong, T.S., Xiong, T.T., Zeng, Z.C., Gan, S.Y., Qiu, C., Du, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.82 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of GPR119-Gs complex

Wong, T.S., Xiong, T.T., Zeng, Z.C.

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: 154.42 kDa 
• Atom Count: 8,018 
• Modeled Residue Count: 1,032 
• Deposited Residue Count: 1,375 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	A	394	Homo sapiens	Mutation(s): 0  Gene Names: 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	384	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
nanobody35	D [auth N]	157	synthetic construct	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-dependent insulinotropic receptor	E [auth R]	369	Homo sapiens	Mutation(s): 0  Gene Names: GPR119
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDV5 (Homo sapiens) Explore Q8TDV5  Go to UniProtKB:  Q8TDV5
PHAROS:  Q8TDV5 GTEx:  ENSG00000147262

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D8Y (Subject of Investigation/LOI)	F [auth R]	GSK-1292263 C23 H28 N4 O4 S AYJRTVVIBJSSKN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.82 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: 2024-06-19 
Deposition Author(s): Wong, T.S., Xiong, T.T., Zeng, Z.C., Gan, S.Y., Qiu, C., Du, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2025-07-16
  Changes: Data collection