8YYW | pdb_00008yyw

Cryo-EM structure of OXGR1 bound to alpha-ketoglutarate and Gq proteins

• PDB DOI: https://doi.org/10.2210/pdb8YYW/pdb
• EM Map EMD-39681: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Vicugna pacos, Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTM


• Deposited: 2024-04-04 Released: 2025-04-09 
• Deposition Author(s): Liu, A., Liu, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.16 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of OXGR1 bound to alpha-ketoglutarate

Liu, A., Liu, Y.

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: 149.04 kDa 
• Atom Count: 9,068 
• Modelled Residue Count: 1,153 
• Deposited Residue Count: 1,334 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ScFv16	A [auth B]	247	Vicugna pacos	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B [auth C]	339	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 D]	57	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
2-oxoglutarate receptor 1	D [auth E]	337	Homo sapiens	Mutation(s): 0  Gene Names: OXGR1, GPR80, GPR99, P2RY15, P2Y15 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q96P68 (Homo sapiens) Explore Q96P68  Go to UniProtKB:  Q96P68
PHAROS:  Q96P68 GTEx:  ENSG00000165621

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha	E [auth F]	354	Homo sapiens	Mutation(s): 2  Gene Names: GNAI1, GNAQ, GAQ 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
Find proteins for P50148 (Homo sapiens) Explore P50148  Go to UniProtKB:  P50148
PHAROS:  P50148 GTEx:  ENSG00000156052
UniProt Groups	P63096P50148

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKG (Subject of Investigation/LOI)	F [auth E], G [auth E]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.16 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-09 
Deposition Author(s): Liu, A., Liu, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-04-09
  Type: Initial release