8YYX | pdb_00008yyx

Cryo-EM structure of OXGR1 bound to leukotriene E4 and Gq proteins

• PDB DOI: https://doi.org/10.2210/pdb8YYX/pdb
• EM Map EMD-39682: EMDB EMDataResource

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


• 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: 2.84 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of OXGR1 bound to leukotriene E4 and Gq proteins

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: 151.15 kDa 
• Atom Count: 9,103 
• Modeled Residue Count: 1,152 
• Deposited Residue Count: 1,348 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
scFV16	A	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	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) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha	C	354	Homo sapiens	Mutation(s): 2  Gene Names: GNAI1, GNAQ, GAQ EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096  Go to UniProtKB:  P63096
PHAROS:  P63096 GTEx:  ENSG00000127955

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
2-oxoglutarate receptor 1	E	337	Homo sapiens	Mutation(s): 0  Gene Names: OXGR1, GPR80, GPR99, P2RY15, P2Y15
UniProt & NIH Common Fund Data Resources
Find proteins for Q96P68 (Homo sapiens) Explore Q96P68  Go to UniProtKB:  Q96P68
PHAROS:  Q96P68 GTEx:  ENSG00000165621

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D7P (Subject of Investigation/LOI)	G [auth E]	(5~{S},6~{R},7~{E},9~{E},11~{Z},14~{Z})-6-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-5-oxidanyl-icosa-7,9,11,14-tetraenoic acid C23 H37 N O5 S OTZRAYGBFWZKMX-FRFVZSDQSA-N
CLR	F [auth E]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.84 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
  
• Version 2.0: 2025-05-28
  Type: Coordinate replacement
  Reason: Ligand identity
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary