9IQT | pdb_00009iqt

structure of niacin-HCA2-Gi

• PDB DOI: https://doi.org/10.2210/pdb9IQT/pdb
• EM Map EMD-60795: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2024-07-13 Released: 2024-10-02 
• Deposition Author(s): Liu, Y., Zhou, Z.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: 3D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Ligand Recognition and Activation Mechanism of the Alicarboxylic Acid Receptors.

Liu, Y., Zhou, Z., Guan, F., Han, Z., Zhu, C., Ye, S., Yu, X., Qiao, A.

(2024) J Mol Biology 436: 168795-168795

• PubMed: 39299383 
• DOI: https://doi.org/10.1016/j.jmb.2024.168795
• Primary Citation of Related Structures:  
  9IQT


• PubMed Abstract: 
  

  Endogenous ligands for alicarboxylic acid receptors are important metabolic intermediates that play a significant role in regulating body energy and maintaining homeostasis. However, the molecular mechanism of alicarboxylate ligand-mediated counterpart receptors is currently unclear. We resolve the active state structure of HCA2-niacin, and the structural analysis explains the mechanism of niacin selectivity in the alicarboxylic acid receptors family. Homology modeling, molecular dynamics simulation and mutagenesis experiments reveal different ligand recognition modes and activation mechanisms of the alicarboxylic acid receptors, analyze the flexibility of the binding pocket and elucidate the important role of disulfide bonds on receptor activation and ligand binding. These more detailed molecular mechanisms further elucidate the relevant mechanisms of human metabolism and provide key clues for subsequent drug development of alicarboxylic acid receptors.

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Organizational Affiliation: 
• Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China.
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
Hangzhou Institute of Medicine, Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou 310000, China.
Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China. Electronic address: [e-mail].
Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China; Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang, China. Electronic address: [e-mail].
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Cryo-Electron Microscopy Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. Electronic address: [e-mail].
Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China. Electronic address: [e-mail].

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: 152.7 kDa 
• Atom Count: 9,095 
• Modeled Residue Count: 1,152 
• Deposited Residue Count: 1,363 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxycarboxylic acid receptor 2	A [auth R]	363	Homo sapiens	Mutation(s): 0  Gene Names: HCAR2, GPR109A, HCA2, HM74A, NIACR1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDS4 (Homo sapiens) Explore Q8TDS4  Go to UniProtKB:  Q8TDS4
PHAROS:  Q8TDS4 GTEx:  ENSG00000182782

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	B [auth A]	352	Homo sapiens	Mutation(s): 0  Gene Names: GNAI1 EC: 3.6.5 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 [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]	61	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	247	Homo sapiens	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: 3D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.14_3260:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): Liu, Y., Zhou, Z.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2020YFA0908500
National Natural Science Foundation of China (NSFC)	China	31971127
National Natural Science Foundation of China (NSFC)	China	32000851

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references
• Version 1.3: 2024-11-13
  Changes: Data collection