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8k5c

Cryo-EM structure of Acipimox bound human hydroxy-carboxylic acid receptor 2 (Local refinement)

Method: ELECTRON MICROSCOPY Dmax: 70.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Human hydroxycarboxylic acid receptor 2

Homo sapiens

UniProt Q8TDS4

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–363 Not recorded OJX 5-methyl-4-oxidanyl-pyrazin-4-ium-2-carboxylic acid × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；20 mM HEPES pH8.0, 100 mM NaCl, 1 mM MgCl2, 0.5 mM TCEP, 0.001% LMNG, 0.0001% CHS cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.13 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8K5C Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7XK2 Cryo-EM Structure of Human Niacin Receptor HCA2-Gi protein complex Deposited 2022-04-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 1–325（325 aa）
Not recorded FI7 2-[[2,2-dimethyl-3-[3-(5-oxidanylpyridin-2-yl)-1,2,4-oxadiazol-5-yl]propanoyl]amino]cyclohexene-1-carboxylic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7ZL9 Crystal structure of human GPCR Niacin receptor (HCA2) Deposited 2022-04-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–325（325 aa）
Not recorded OLA OLEIC ACID × 5 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 PEG DI(HYDROXYETHYL)ETHER × 1 UNX UNKNOWN LIGAND × 5 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100mM pH5.4 sodium citrate, 60mM ammonium citrate, 36% PEG400, and 3% Additive 80 (40% PPG)
Resolution 2.70 Å R-free 0.248
7ZLY Crystal structure of human GPCR Niacin receptor (HCA2) expressed from Spodoptera frugiperda Deposited 2022-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–219（219 aa）
Chain A 220–325（106 aa）
Not recorded OLA OLEIC ACID × 6 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；100mM pH5.4 sodium citrate, 60mM ammonium citrate, 36% PEG400, and 3% Additive 80 (40% PPG)
Resolution 2.70 Å R-free 0.280
8H2G Cryo-EM structure of niacin bound human hydroxy-carboxylic acid receptor 2 in complex with Gi heterotrimer Deposited 2022-10-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–363（363 aa）
Not recorded NIO NICOTINIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH8.0, 100 mM NaCl, 1 mM MgCl2, 0.5 mM TCEP, 0.001% LMNG, 0.0001% CHS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.01 Å
8I7V Cryo-EM structure of Acipimox bound human hydroxy-carboxylic acid receptor 2 in complex with Gi heterotrimer Deposited 2023-02-02 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–363（363 aa）
Not recorded OJX 5-methyl-4-oxidanyl-pyrazin-4-ium-2-carboxylic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH8.0, 100 mM NaCl, 1 mM MgCl2, 0.5 mM TCEP, 0.001% LMNG, 0.0001% CHS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.77 Å
8I7W Cryo-EM structure of GSK256073 bound human hydroxy-carboxylic acid receptor 2 in complex with Gi heterotrimer Deposited 2023-02-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–363（363 aa）
Not recorded OKL 8-chloranyl-3-pentyl-7H-purine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
8IHB Cryo-EM structure of HCA2-Gi complex with GSK256073 Deposited 2023-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 2–363（362 aa）
Mutation：M29W,H124I NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 OKL 8-chloranyl-3-pentyl-7H-purine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
8IHF Cryo-EM structure of HCA2-Gi complex with MK6892 Deposited 2023-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 2–363（362 aa）
Mutation：M29W,H124I NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 FI7 2-[[2,2-dimethyl-3-[3-(5-oxidanylpyridin-2-yl)-1,2,4-oxadiazol-5-yl]propanoyl]amino]cyclohexene-1-carboxylic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.97 Å
8IHH Cryo-EM structure of HCA2-Gi complex with LUF6283 Deposited 2023-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 2–363（362 aa）
Mutation：M29W,H124I NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 P8A 5-butyl-1~{H}-pyrazole-3-carboxylic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.06 Å
8IHI Cryo-EM structure of HCA2-Gi complex with acifran Deposited 2023-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 2–363（362 aa）
Mutation：M29W,H124I NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 P9X (5~{S})-5-methyl-4-oxidanylidene-5-phenyl-furan-2-carboxylic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
8IJ3 Cryo-EM structure of human HCAR2-Gi complex without ligand (apo state) Deposited 2023-02-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 8–299（292 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.28 Å
8IJA Cryo-EM structure of human HCAR2-Gi complex with niacin Deposited 2023-02-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 8–301（294 aa）
Not recorded NIO NICOTINIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.69 Å
8IJB Cryo-EM structure of human HCAR2-Gi complex with acipimox Deposited 2023-02-27 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 8–301（294 aa）
Not recorded OJX 5-methyl-4-oxidanyl-pyrazin-4-ium-2-carboxylic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.23 Å
8IJD Cryo-EM structure of human HCAR2-Gi complex with MK-6892 Deposited 2023-02-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 8–301（294 aa）
Not recorded FI7 2-[[2,2-dimethyl-3-[3-(5-oxidanylpyridin-2-yl)-1,2,4-oxadiazol-5-yl]propanoyl]amino]cyclohexene-1-carboxylic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.25 Å
8IY9 Structure of Niacin-GPR109A-G protein complex Deposited 2023-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 2–363（362 aa）
Not recorded NIO NICOTINIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å
8IYH Structure of MK6892-GPR109A-G-protein complex Deposited 2023-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 2–363（362 aa）
Not recorded FI7 2-[[2,2-dimethyl-3-[3-(5-oxidanylpyridin-2-yl)-1,2,4-oxadiazol-5-yl]propanoyl]amino]cyclohexene-1-carboxylic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8IYW Structure of GSK256073-GPR109A-G-protein complex Deposited 2023-04-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 2–363（362 aa）
Not recorded OKL 8-chloranyl-3-pentyl-7H-purine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
8J6I Cryo-EM structure of thehydroxycarboxylic acid receptor 2-Gi protein complex bound MK-6892 Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 1–311（311 aa）
Not recorded FI7 2-[[2,2-dimethyl-3-[3-(5-oxidanylpyridin-2-yl)-1,2,4-oxadiazol-5-yl]propanoyl]amino]cyclohexene-1-carboxylic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.92 Å
8J6J Cryo-EM structure of thehydroxycarboxylic acid receptor 2-Gi protein complex bound with GSK256073 Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 1–330（330 aa）
Not recorded OKL 8-chloranyl-3-pentyl-7H-purine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8J6L Cryo-EM structure of thehydroxycarboxylic acid receptor 2-Gi protein complex bound niacin Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 1–330（330 aa）
Not recorded NIO NICOTINIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8J6P Cryo-EM structure of the MK-6892-bound human HCAR2-Gi1 complex Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 8–301（294 aa）
Not recorded IX8 7-methyl-N-[(2R)-1-phenoxypropan-2-yl]-3-(4-propan-2-ylphenyl)pyrazolo[1,5-a]pyrimidine-6-carboxamide × 1 CLR CHOLESTEROL × 2 NIO NICOTINIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.55 Å
8J6Q Cryo-EM structure of the 3-HB and compound 9n-bound human HCAR2-Gi1 complex Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 8–301（294 aa）
Not recorded IX8 7-methyl-N-[(2R)-1-phenoxypropan-2-yl]-3-(4-propan-2-ylphenyl)pyrazolo[1,5-a]pyrimidine-6-carboxamide × 1 CLR CHOLESTEROL × 2 3HR (3R)-3-hydroxybutanoic acid × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8J6R Cryo-EM structure of the MK-6892-bound human HCAR2-Gi1 complex Deposited 2023-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 8–301（294 aa）
Not recorded FI7 2-[[2,2-dimethyl-3-[3-(5-oxidanylpyridin-2-yl)-1,2,4-oxadiazol-5-yl]propanoyl]amino]cyclohexene-1-carboxylic acid × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
8JER Structure of Acipimox-GPR109A-G protein complex Deposited 2023-05-16 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 2–363（362 aa）
Not recorded OJX 5-methyl-4-oxidanyl-pyrazin-4-ium-2-carboxylic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
8JHN Structure of MMF-GPR109A-G protein complex Deposited 2023-05-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 2–363（362 aa）
Not recorded UR9 Monomethyl fumarate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.75 Å
8JHY Cryo-EM structure of compound 9n bound ketone body receptor HCAR2-Gi signaling complex Deposited 2023-05-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–363（363 aa）
Not recorded IX8 7-methyl-N-[(2R)-1-phenoxypropan-2-yl]-3-(4-propan-2-ylphenyl)pyrazolo[1,5-a]pyrimidine-6-carboxamide × 1 CLR CHOLESTEROL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8JII Cryo-EM structure of compound 9n and niacin bound ketone body receptor HCAR2-Gi signaling complex Deposited 2023-05-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–363（363 aa）
Not recorded NIO NICOTINIC ACID × 1 CLR CHOLESTEROL × 1 IX8 7-methyl-N-[(2R)-1-phenoxypropan-2-yl]-3-(4-propan-2-ylphenyl)pyrazolo[1,5-a]pyrimidine-6-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
8JIL Cryo-EM structure of niacin bound ketone body receptor HCAR2-Gi signaling complex Deposited 2023-05-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–363（363 aa）
Not recorded NIO NICOTINIC ACID × 1 CLR CHOLESTEROL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8JIM Cryo-EM structure of MMF bound ketone body receptor HCAR2-Gi signaling complex Deposited 2023-05-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–363（363 aa）
Not recorded AW9 (2Z)-4-methoxy-4-oxobut-2-enoic acid × 1 CLR CHOLESTEROL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
8JZ7 Cryo-EM structure of MK-6892-bound HCAR2 in complex with Gi protein Deposited 2023-07-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–363（363 aa）
Not recorded FI7 2-[[2,2-dimethyl-3-[3-(5-oxidanylpyridin-2-yl)-1,2,4-oxadiazol-5-yl]propanoyl]amino]cyclohexene-1-carboxylic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8K5B Cryo-EM structure of niacin bound human hydroxy-carboxylic acid receptor 2 (Local refinement) Deposited 2023-07-21 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–363（363 aa）
Not recorded NIO NICOTINIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH8.0, 100 mM NaCl, 1 mM MgCl2, 0.5 mM TCEP, 0.001% LMNG, 0.0001% CHS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.43 Å
8K5D Cryo-EM structure of GSK256073 bound human hydroxy-carboxylic acid receptor 2 (Local refinement) Deposited 2023-07-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–363（363 aa）
Not recorded OKL 8-chloranyl-3-pentyl-7H-purine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.74 Å
8UTD CryoEM Structure of HCA2-Gi1 in complex with MK-1903 Deposited 2023-10-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 1–363（363 aa）
Mutation：D124A XOT (4aR,5aR)-4,4a,5,5a-tetrahydro-1H-cyclopropa[4,5]cyclopenta[1,2-c]pyrazole-3-carboxylic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.24 Å
9IQT structure of niacin-HCA2-Gi Deposited 2024-07-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 1–363（363 aa）
Not recorded NIO NICOTINIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9IZA Cryo-EM structure of human HCAR2-Gi complex with SCH900271 Deposited 2024-08-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 8–301（294 aa）
Not recorded A1EAD SCH-900271 × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.06 Å
9IZC Cryo-EM structure of human HCAR2-Gi complex with MK1903 Deposited 2024-08-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 8–301（294 aa）
Not recorded XOT (4aR,5aR)-4,4a,5,5a-tetrahydro-1H-cyclopropa[4,5]cyclopenta[1,2-c]pyrazole-3-carboxylic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.68 Å
9JKY acifran-HCAR2-Gi complex Deposited 2024-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 8–301（294 aa）
Not recorded P9X (5~{S})-5-methyl-4-oxidanylidene-5-phenyl-furan-2-carboxylic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
9KT7 Cryo-EM structure of HCA2-Gi complex with MK6892 Deposited 2024-12-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 1–363（363 aa）
Not recorded FI7 2-[[2,2-dimethyl-3-[3-(5-oxidanylpyridin-2-yl)-1,2,4-oxadiazol-5-yl]propanoyl]amino]cyclohexene-1-carboxylic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9KT8 Cryo-EM structure of HCA2-Gi complex with acifran Deposited 2024-12-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 1–363（363 aa）
Not recorded P9X (5~{S})-5-methyl-4-oxidanylidene-5-phenyl-furan-2-carboxylic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.73 Å

39 other PDB entries and 39 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HCAR2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 114–476； UniProt 1–363

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8k5c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8k5c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8k5c
Deposition date deposition_date2023-07-21
Structure title titleCryo-EM structure of Acipimox bound human hydroxy-carboxylic acid receptor 2 (Local refinement)
Keywords keywordsGPCR, G-Protein, MEMBRANE PROTEIN, acipimox, signaling; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.04 Å
Radius of gyration Rg (electron density) rg_electron20.73 Å
Forward intensity I(0) i016517800.00
Molecular weight molecular_weight33755.0 kDa
Excluded volume excluded_volume43566 ų
Envelope volume envelope_volume50288 ų
Hydration-shell volume shell_volume20713 ų
Envelope diameter envelope_diameter72.7 Å
Shell Rg shell_rg27.05 Å
Envelope Rg envelope_rg21.10 Å
Shape Rg shape_rg20.73 Å
Total Rg total_rg21.69 Å
Total atoms total_atoms2380
Residues n_residues291
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax70.5 Å
Rg (real space) rg_real22.11 Å
Rg uncertainty (real space) rg_real_error0.49 Å
I(0) (real space) i0_real1.6520e+07
I(0) uncertainty (real space) i0_real_error2.2630e+05
Rg (reciprocal space) rg_reciprocal22.09 Å
I(0) (reciprocal space) i0_reciprocal16520000.0000
Solution quality estimate total_estimate0.8916
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.2 Å
Skewness Skewness skewness0.406
Kurtosis Kurtosis kurtosis-0.402
Angular range angular_range— – 0.3600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2630000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.988
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)