9IZG

Cryo-EM structure of LPA1-Gq complex with LPA

• PDB DOI: https://doi.org/10.2210/pdb9IZG/pdb
• EM Map EMD-61032: EMDB EMDataResource

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


• Deposited: 2024-08-01 Released: 2025-01-01 
• Deposition Author(s): Suzuki, S., Nishikawa, K., Kmegawa, A., Hiroaki, Y., Suzuki, H., Fujiyoshi, Y.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into the engagement of lysophosphatidic acid receptor 1 with different G proteins

Suzuki, S., Kamegawa, A., Hiroaki, Y., Tanaka, K., Nishikawa, K., suzuki, H., Numoto, N., Sasaki, D., Oshima, A., Fujiyoshi, 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: 177.68 kDa 
• Atom Count: 8,702 
• Modelled Residue Count: 1,149 
• Deposited Residue Count: 1,597 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	A [auth B]	382	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	B [auth C]	70	Mus musculus	Mutation(s): 0  Gene Names: Gng2
UniProt
Find proteins for P63213 (Mus musculus) Explore P63213  Go to UniProtKB:  P63213

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,Lysophosphatidic acid receptor 1,LgBiT tag	C [auth R]	651	Escherichia coli, Homo sapiens, synthetic construct This entity is chimeric	Mutation(s): 0  Gene Names: cybC, LPAR1, EDG2, LPA1
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for Q92633 (Homo sapiens) Explore Q92633  Go to UniProtKB:  Q92633
PHAROS:  Q92633 GTEx:  ENSG00000198121
UniProt Groups	P0ABE7Q92633

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Gs-mini-Gq chimera	D [auth A]	246	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	E [auth S]	248	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NKP (Subject of Investigation/LOI)	F [auth R]	(2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate C21 H41 O7 P WRGQSWVCFNIUNZ-SQUSKLHYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-01 
Deposition Author(s): Suzuki, S., Nishikawa, K., Kmegawa, A., Hiroaki, Y., Suzuki, H., Fujiyoshi, Y.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	20H00451

Revision History  

• Version 1.0: 2025-01-01
  Type: Initial release