9GGG | pdb_00009ggg

Cryo-EM structure of Thromboxane A2 receptor-miniGq Protein Complex bound to I-BOP

• PDB DOI: https://doi.org/10.2210/pdb9GGG/pdb
• EM Map EMD-51331: EMDB EMDataResource

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


• Deposited: 2024-08-13 Released: 2025-08-27 
• Deposition Author(s): Matzov, D., Krawinski, P., Caffrey, M., Shalev Benami, M.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of Thromboxane A2 receptor-miniGq Protein Complex bound to I-BOP

Krawinski, P., Matzov, D., Ryder, A., Lal, K., Karlov, D.S., Chalhoub, G., McCormick, P.J., Caffrey, M., Tikhonova, I.G., Shalev Benami, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 140.23 kDa 
• Atom Count: 8,656 
• Modeled Residue Count: 1,159 
• Deposited Residue Count: 1,256 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thromboxane A2 receptor	A [auth R]	343	Homo sapiens	Mutation(s): 0  Gene Names: TBXA2R
UniProt & NIH Common Fund Data Resources
Find proteins for P21731 (Homo sapiens) Explore P21731  Go to UniProtKB:  P21731
PHAROS:  P21731 GTEx:  ENSG00000006638

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Engineered miniGq	B [auth A]	246	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for A0A804HIH4 (Homo sapiens) Explore A0A804HIH4  Go to UniProtKB:  A0A804HIH4
GTEx:  ENSG00000087460

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C [auth B]	340	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D [auth C]	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
Antibody fragment scFv16	E [auth S]	256	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IK0 (Subject of Investigation/LOI)	F [auth R]	(~{Z})-7-[(1~{S},2~{R},3~{R},4~{R})-3-[(~{E},3~{R})-4-(4-iodanylphenoxy)-3-oxidanyl-but-1-enyl]-7-oxabicyclo[2.2.1]heptan-2-yl]hept-5-enoic acid C23 H29 I O5 UYFMSCHBODMWON-HBHIRWTLSA-N
CLR	G [auth R], H [auth R], I [auth R], J [auth R]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-27 
Deposition Author(s): Matzov, D., Krawinski, P., Caffrey, M., Shalev Benami, M.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	949364

Revision History  

• Version 1.0: 2025-08-27
  Type: Initial release