8IHB

Cryo-EM structure of HCA2-Gi complex with GSK256073

• PDB DOI:  https://doi.org/10.2210/pdb8IHB/pdb
• EM Map EMD-35442: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Escherichia coli, Homo sapiens, synthetic construct, Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2023-02-22 Released: 2023-09-13 
• Deposition Author(s): Suzuki, S., Nishikawa, K., 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: 2.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of signaling mechanisms of Hydroxycarboxylic acid receptors through ligand binding

Suzuki, S., Tanaka, K., Nishikawa, K., Suzuki, H., 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: gel filtration

Macromolecule Content

• Total Structure Weight: 191.7 kDa 
• Atom Count: 8,708 
• Modelled Residue Count: 1,131 
• Deposited Residue Count: 1,711 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,Hydroxycarboxylic acid receptor 2	A [auth R]	658	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 2  Gene Names: cybC, HCAR2, GPR109A, HCA2, HM74A, NIACR1
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for Q8TDS4 (Homo sapiens) Explore Q8TDS4  Go to UniProtKB:  Q8TDS4
PHAROS:  Q8TDS4
UniProt Groups	P0ABE7Q8TDS4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	B [auth A]	354	Homo sapiens	Mutation(s): 2  Gene Names: GNAI1
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096  Go to UniProtKB:  P63096
PHAROS:  P63096

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	C [auth S]	248	synthetic construct	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	D [auth B]	382	Mus musculus	Mutation(s): 0  Gene Names: Gnb1
UniProt & NIH Common Fund Data Resources
Find proteins for P62874 (Mus musculus) Explore P62874  Go to UniProtKB:  P62874
IMPC:  MGI:95781

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	E [auth C]	69	Mus musculus	Mutation(s): 0  Gene Names: Gng2
UniProt
Find proteins for P63213 (Mus musculus) Explore P63213  Go to UniProtKB:  P63213

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OKL (Subject of Investigation/LOI)	G [auth R]	8-chloranyl-3-pentyl-7H-purine-2,6-dione C10 H13 Cl N4 O2 CGAMDQCXAAOFSR-UHFFFAOYSA-N
NAG	F [auth R]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-13 
Deposition Author(s): Suzuki, S., Nishikawa, K., 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: 2023-09-13
  Type: Initial release