9j7i

Cryo-EM Structure of calcium sensing receptor in complex gamma-glutamyl-valyl-glycine as a kokumi substance

Method: ELECTRON MICROSCOPY D_max: 75.8 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Extracellular calcium-sensing receptor

Homo sapiens

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 19–894	Not recorded	gamma-glutamyl-valyl-glycine × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.55 Å
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 19–894	Not recorded	gamma-glutamyl-valyl-glycine × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.55 Å
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 19–894	Not recorded	gamma-glutamyl-valyl-glycine × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.55 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 9J7I	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5FBH Crystal structure of the extracellular domain of human calcium sensing receptor with bound Gd3+ Deposited 2015-12-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–541（522 aa） Fragment：UNP residues 20-541 Chain B 20–541（522 aa） Fragment：UNP residues 20-541	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	GD3 GADOLINIUM ION × 2 MG MAGNESIUM ION × 3 BCT BICARBONATE ION × 2 CL CHLORIDE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 TCR CYCLOMETHYLTRYPTOPHAN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；10% PEG 8000, 200 mM MgCl2, 10 mM CaCl2 and 100 mM Tris-HCl, 0.5 mM GdCl3	Resolution 2.70 Å R-free 0.236
5FBK Crystal structure of the extracellular domain of human calcium sensing receptor Deposited 2015-12-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–541（522 aa） Fragment：UNP residues 20-541 Chain B 20–541（522 aa） Fragment：UNP residues 20-541	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	TCR CYCLOMETHYLTRYPTOPHAN × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CL CHLORIDE ION × 6 BCT BICARBONATE ION × 2 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；10% PEG 8000, 200 mM MgCl2, 10 mM CaCl2 and 100 mM Tris-HCl	Resolution 2.10 Å R-free 0.223
5K5S Crystal structure of the active form of human calcium-sensing receptor extracellular domain Deposited 2016-05-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–607（588 aa） Chain B 20–607（588 aa）	Not recorded	TRP TRYPTOPHAN × 2 PO4 PHOSPHATE ION × 4 CA CALCIUM ION × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.6 M NaH2PO4, 0.4 M K2HPO4, 100 mM Na2HPO4/citric acid pH 4.2, 10 mM CaCl2, 10 mM L-Trp	Resolution 2.60 Å R-free 0.222
5K5T Crystal structure of the inactive form of human calcium-sensing receptor extracellular domain Deposited 2016-05-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–607（588 aa）	Not recorded	CA CALCIUM ION × 2 SO4 SULFATE ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.5 M Li2SO4, 100 mM Tris pH 8.5, 2 mM CaCl2	Resolution 3.10 Å R-free 0.239
5K5T Crystal structure of the inactive form of human calcium-sensing receptor extracellular domain Deposited 2016-05-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–607（588 aa）	Not recorded	CA CALCIUM ION × 2 SO4 SULFATE ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.5 M Li2SO4, 100 mM Tris pH 8.5, 2 mM CaCl2	Resolution 3.10 Å R-free 0.239
5K5T Crystal structure of the inactive form of human calcium-sensing receptor extracellular domain Deposited 2016-05-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 20–607（588 aa）	Not recorded	CA CALCIUM ION × 4 SO4 SULFATE ION × 12 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.5 M Li2SO4, 100 mM Tris pH 8.5, 2 mM CaCl2	Resolution 3.10 Å R-free 0.239
7DTT Human Calcium-Sensing Receptor bound with calcium ions Deposited 2021-01-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–1078（1059 aa） Chain B 20–1078（1059 aa）	Not recorded	CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7DTU Human Calcium-Sensing Receptor bound with L-Trp Deposited 2021-01-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–1078（1059 aa） Chain B 20–1078（1059 aa）	Not recorded	TRP TRYPTOPHAN × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
7DTV Human Calcium-Sensing Receptor bound with L-Trp and calcium ions Deposited 2021-01-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–1078（1059 aa） Chain B 20–1078（1059 aa）	Not recorded	TRP TRYPTOPHAN × 2 CA CALCIUM ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7DTW Human Calcium-Sensing Receptor in the inactive close-close conformation Deposited 2021-01-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–1078（1059 aa） Chain B 20–1078（1059 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
7E6T Structural insights into the activation of human calcium-sensing receptor Deposited 2021-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–870（851 aa） Chain B 20–870（851 aa）	Not recorded	PO4 PHOSPHATE ION × 2 CA CALCIUM ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 TCR CYCLOMETHYLTRYPTOPHAN × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.00 Å
7E6U the complex of inactive CaSR and NB2D11 Deposited 2021-02-24	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 20–870（851 aa） Chain C 20–870（851 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 6.00 Å
7M3E Asymmetric Activation of the Calcium Sensing Receptor Homodimer Deposited 2021-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–894（875 aa） Chain B 20–894（875 aa）	Not recorded	YP1 2-chloro-6-[(2R)-2-hydroxy-3-{[2-methyl-1-(naphthalen-2-yl)propan-2-yl]amino}propoxy]benzonitrile × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 TRP TRYPTOPHAN × 2 CA CALCIUM ION × 4 PO4 PHOSPHATE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7M3F Asymmetric Activation of the Calcium Sensing Receptor Homodimer Deposited 2021-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–894（875 aa） Chain B 20–894（875 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 YP4 N-[(1R)-1-(naphthalen-1-yl)ethyl]-3-[3-(trifluoromethyl)phenyl]propan-1-amine × 2 TRP TRYPTOPHAN × 2 CA CALCIUM ION × 4 PO4 PHOSPHATE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7M3G Asymmetric Activation of the Calcium Sensing Receptor Homodimer Deposited 2021-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 20–894（875 aa） Chain B 20–894（875 aa）	Not recorded	H43 2-[4-[(3S)-3-[[(1R)-1-naphthalen-1-ylethyl]amino]pyrrolidin-1-yl]phenyl]ethanoic acid × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 TRP TRYPTOPHAN × 2 CA CALCIUM ION × 4 PO4 PHOSPHATE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
7M3J Asymmetric Activation of the Calcium Sensing Receptor Homodimer Deposited 2021-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–894（875 aa） Chain B 20–894（875 aa）	Not recorded	YP1 2-chloro-6-[(2R)-2-hydroxy-3-{[2-methyl-1-(naphthalen-2-yl)propan-2-yl]amino}propoxy]benzonitrile × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 PO4 PHOSPHATE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
8SZF Cryo-EM structure of cinacalcet-bound active-state human calcium-sensing receptor CaSR in lipid nanodiscs Deposited 2023-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 19–894（876 aa） Chain B 19–894（876 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 TRP TRYPTOPHAN × 2 CA CALCIUM ION × 4 PO4 PHOSPHATE ION × 2 YP4 N-[(1R)-1-(naphthalen-1-yl)ethyl]-3-[3-(trifluoromethyl)phenyl]propan-1-amine × 2 SPM SPERMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8SZG Cryo-EM structure of cinacalcet-bound human calcium-sensing receptor CaSR-Gq complex in lipid nanodiscs Deposited 2023-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 19–894（876 aa） Chain B 19–894（876 aa）	Not recorded	YP4 N-[(1R)-1-(naphthalen-1-yl)ethyl]-3-[3-(trifluoromethyl)phenyl]propan-1-amine × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 SPM SPERMINE × 3 CA CALCIUM ION × 3 TRP TRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8SZH Cryo-EM structure of cinacalcet-bound human calcium-sensing receptor CaSR-Gi complex in lipid nanodiscs Deposited 2023-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 19–894（876 aa） Chain B 19–894（876 aa）	Not recorded	YP4 N-[(1R)-1-(naphthalen-1-yl)ethyl]-3-[3-(trifluoromethyl)phenyl]propan-1-amine × 2 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 4 TRP TRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 SPM SPERMINE × 4 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8SZI Cryo-EM structure of PAM-free human calcium-sensing receptor CaSR-Gi complex in lipid nanodiscs Deposited 2023-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 19–894（876 aa） Chain B 19–894（876 aa）	Not recorded	PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 4 TRP TRYPTOPHAN × 3 PO4 PHOSPHATE ION × 2 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8WPG Human calcium-sensing receptor bound with cinacalcet in detergent Deposited 2023-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–892（873 aa） Chain B 20–892（873 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 TRP TRYPTOPHAN × 2 CA CALCIUM ION × 4 PO4 PHOSPHATE ION × 2 YP4 N-[(1R)-1-(naphthalen-1-yl)ethyl]-3-[3-(trifluoromethyl)phenyl]propan-1-amine × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8WPU Human calcium-sensing receptor(CaSR) bound to cinacalcet in complex with Gq protein Deposited 2023-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 20–892（873 aa） Chain B 20–892（873 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 YP4 N-[(1R)-1-(naphthalen-1-yl)ethyl]-3-[3-(trifluoromethyl)phenyl]propan-1-amine × 2 TRP TRYPTOPHAN × 2 CA CALCIUM ION × 4 PO4 PHOSPHATE ION × 2 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9ASB Structure of human calcium-sensing receptor in complex with chimeric Gq (miniGisq) protein in nanodiscs Deposited 2024-02-24	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 Q 1–903（903 aa） Chain R 1–903（903 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 TCR CYCLOMETHYLTRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 CA CALCIUM ION × 6 9IG 3-(2-chlorophenyl)-N-[(1R)-1-(3-methoxyphenyl)ethyl]propan-1-amine × 2 Y01 CHOLESTEROL HEMISUCCINATE × 1 A1AF7 (19R,22S,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9Z)-octadec-9-enoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；The sample was blotted for 6s before plunge-frozen.	Resolution 3.40 Å
9AVG Structure of human calcium-sensing receptor in complex with chimeric Gs (miniGis) protein in nanodiscs Deposited 2024-03-02	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 Q 1–903（903 aa） Chain R 1–903（903 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 TCR CYCLOMETHYLTRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 CA CALCIUM ION × 6 9IG 3-(2-chlorophenyl)-N-[(1R)-1-(3-methoxyphenyl)ethyl]propan-1-amine × 2 Y01 CHOLESTEROL HEMISUCCINATE × 1 A1AF7 (19R,22S,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9Z)-octadec-9-enoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；The sample was blotted for 6s before plunge-frozen.	Resolution 3.60 Å
9AVL Structure of human calcium-sensing receptor in complex with Gi3 protein in nanodiscs Deposited 2024-03-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain Q 1–903（903 aa） Chain R 1–903（903 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 TCR CYCLOMETHYLTRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 CA CALCIUM ION × 6 9IG 3-(2-chlorophenyl)-N-[(1R)-1-(3-methoxyphenyl)ethyl]propan-1-amine × 2 Y01 CHOLESTEROL HEMISUCCINATE × 1 A1AF7 (19R,22S,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosphahexacosan-19-yl (9Z)-octadec-9-enoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；The sample was blotted for 6s before plunge-frozen.	Resolution 3.80 Å
9AXF Structure of human calcium-sensing receptor in complex with chimeric Gq (miniGisq) protein in detergent Deposited 2024-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric	Chain Q 1–903（903 aa） Chain R 1–903（903 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 TCR CYCLOMETHYLTRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 CA CALCIUM ION × 7 9IG 3-(2-chlorophenyl)-N-[(1R)-1-(3-methoxyphenyl)ethyl]propan-1-amine × 2 AV0 Lauryl Maltose Neopentyl Glycol × 1 Y01 CHOLESTEROL HEMISUCCINATE × 4 CLR CHOLESTEROL × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；The sample was blotted for 6s before plunge-frozen.	Resolution 3.50 Å
9AYF Structure of human calcium-sensing receptor in complex with Gi1 (miniGi1) protein in detergent Deposited 2024-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain Q 1–903（903 aa） Chain R 1–903（903 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 TCR CYCLOMETHYLTRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 CA CALCIUM ION × 8 9IG 3-(2-chlorophenyl)-N-[(1R)-1-(3-methoxyphenyl)ethyl]propan-1-amine × 2 AV0 Lauryl Maltose Neopentyl Glycol × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；The sample was blotted for 6s before plunge-frozen.	Resolution 3.60 Å
9C1P Structure of Calcium-Sensing Receptor in complex with positive allosteric modulator '6218 Deposited 2024-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 19–894（876 aa） Chain B 19–894（876 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 8 TRP TRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 A1ATP (5R)-N-[2-(1,2-benzothiazol-3-yl)ethyl]-1-methyl-2,3,4,5-tetrahydro-1H-1-benzazepin-5-amine × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9C2F Structure of Calcium-Sensing Receptor in complex with positive allosteric modulator '54149 Deposited 2024-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 19–894（876 aa） Chain B 19–894（876 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CA CALCIUM ION × 8 TRP TRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 A1ATX (1R)-1-(2H-1,3-benzodioxol-4-yl)-N-[2-(1,2-benzothiazol-3-yl)ethyl]ethan-1-amine × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å

27 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CASR_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 27–902； UniProt 19–894

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9j7i
Deposition date deposition_date	2024-08-19
最后修订 last_revision	2025-02-19
Structure title title	Cryo-EM Structure of calcium sensing receptor in complex gamma-glutamyl-valyl-glycine as a kokumi substance
Keywords keywords	complex, agonist, calcium-sensing receptor, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	23.86 Å
Radius of gyration Rg (electron density) rg_electron	22.67 Å
Forward intensity I(0) i0	42592300.00
Molecular weight molecular_weight	51488.0 kDa
Excluded volume excluded_volume	64840 Å³
Envelope volume envelope_volume	76241 Å³
Hydration-shell volume shell_volume	27584 Å³
Envelope diameter envelope_diameter	76.3 Å
Shell Rg shell_rg	30.12 Å
Envelope Rg envelope_rg	23.04 Å
Shape Rg shape_rg	22.65 Å
Total Rg total_rg	23.64 Å
Total atoms total_atoms	3642
Residues n_residues	458
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	75.8 Å
Rg (real space) rg_real	23.78 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	4.2590e+07
I(0) uncertainty (real space) i0_real_error	5.1660e+05
Rg (reciprocal space) rg_reciprocal	23.80 Å
I(0) (reciprocal space) i0_reciprocal	42590000.0000
Solution quality estimate total_estimate	0.8968
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.4 Å
Skewness Skewness skewness	0.281
Kurtosis Kurtosis kurtosis	-0.354
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	10550000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.993

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Extracellular calcium-sensing receptor
Molecular weight formula_weight	101745.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3642

MKTIIALSYIFCLVFADYKDDDDKAAAYGPDQRAQKKGDIILGGLFPIHFGVAAKDQDLKSRPESVECIRYNFRGFRWLQAMIFAIEEINSSPALLPNLTLGYRIFDTCNTVSKALEATLSFVAQNKIDSLNLDEFCNCSEHIPSTIAVVGATGSGVSTAVANLLGLFYIPQVSYASSSRLLSNKNQFKSFLRTIPNDEHQATAMADIIEYFRWNWVGTIAADDDYGRPGIEKFREEAEERDICIDFSELISQYSDEEEIQHVVEVIQNSTAKVIVVFSSGPDLEPLIKEIVRRNITGKIWLASEAWASSSLIAMPQYFHVVGGTIGFALKAGQIPGFREFLKKVHPRKSVHNGFAKEFWEETFNCHLQEGAKGPLPVDTFLRGHEESGDRFSNSSTAFRPLCTGDENISSVETPYIDYTHLRISYNVYLAVYSIAHALQDIYTCLPGRGLFTNGSCADIKKVEAWQVLKHLRHLNFTNNMGEQVTFDECGDLVGNYSIINWHLSPEDGSIVFKEVGYYNVYAKKGERLFINEEKILWSGFSREVPFSNCSRDCLAGTRKGIIEGEPTCCFECVECPDGEYSDETDASACNKCPDDFWSNENHTSCIAKEIEFLSWTEPFGIALTLFAVLGIFLTAFVLGVFIKFRNTPIVKATNRELSYLLLFSLLCCFSSSLFFIGEPQDWTCRLRQPAFGISFVLCISCILVKTNRVLLVFEAKIPTSFHRKWWGLNLQFLLVFLCTFMQIVICVIWLYTAPPSSYRNQELEDEIIFITCHEGSLMALGFLIGYTCLLAAICFFFAFKSRKLPENFNEAKFITFSMLIFFIVWISFIPAYASTYGKFVSAVEVIAILAASFGLLACIFFNKIYIILFKPSRNTIEEVRCSTAAHAFKVAARATLRRSNV

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	gamma-glutamyl-valyl-glycine
Molecular weight formula_weight	303.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

EVG

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.55 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	177479

fit	/app/data/saxs_computation/j7/9j7i/9j7i.fit
pddf	/app/data/pr_computation/j7/9j7i/9j7i.pr.out
profile	/app/data/saxs_computation/j7/9j7i/9j7i.dat

Cryo-EM Structure of calcium sensing receptor in complex gamma-glutamyl-valyl-glycine as a kokumi substance

1. Protein Identity and Related Structures Protein Identity & Related Structures

Extracellular calcium-sensing receptor

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)