8H2G

Cryo-EM structure of niacin bound human hydroxy-carboxylic acid receptor 2 in complex with Gi heterotrimer

• PDB DOI: https://doi.org/10.2210/pdb8H2G/pdb
• EM Map EMD-34437: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2022-10-06 Released: 2023-10-11 
• Deposition Author(s): Park, J.H., Ishimoto, N., Park, S.Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.01 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for hydroxy-carboxylic acid receptor 2 activation and allosteric mechanism

Park, J.H., Ishimoto, N., Kawakami, K., Ikuta, T., Ohki, M., Ekimoto, T., Ikeguchi, M., Lee, D.S., Lee, Y.H., Tame, J.R.H., Inoue, A., Park, S.Y.

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)

Macromolecule Content

• Total Structure Weight: 168.5 kDa 
• Atom Count: 9,023 
• Modelled Residue Count: 1,145 
• Deposited Residue Count: 1,512 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxy-carboxylic acid receptor 2	A	476	Homo sapiens	Mutation(s): 0  Gene Names: HCAR2, HCA2 Membrane Entity: Yes
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 GTEx:  ENSG00000182782
UniProt Groups	P0ABE7Q8TDS4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	B	354	Homo sapiens	Mutation(s): 0  Gene Names: GNAI1 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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	345	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	80	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	E	257	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NIO (Subject of Investigation/LOI)	F [auth A]	NICOTINIC ACID C6 H5 N O2 PVNIIMVLHYAWGP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.01 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-11 
Deposition Author(s): Park, J.H., Ishimoto, N., Park, S.Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-10-11
  Type: Initial release