4l4h

Crystal structure of mouse Ryanodine Receptor isoform 2 (RyR2) 1-547

Method: X-RAY DIFFRACTION D_max: 74.8 Å Quality: EXCELLENT

▼

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

Ryanodine receptor 2

Mus musculus

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 1–547	Fragment：N-terminal domains (UNP residues 1-547)	CL CHLORIDE ION × 1 PGE TRIETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.15；294 K；6% PEG3350, 0.1 M Tris, pH 8.15, 0.8% ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K	Resolution 2.00 Å R-free 0.251

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 4L4H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2MC2 X-ray crystallography-solution NMR hybrid structure of mouse RyR2 domain A Deposited 2013-08-13	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 10–224（215 aa） Fragment：domain A (UNP residues 10-224)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；288 K；Ionic strength (raw mmCIF value) 0.328；Pressure ambient NMR sample composition 0.4 mM [U-13C; U-15N; U-2H] RyR2, 20 mM sodium phosphate, 300 mM sodium chloride, 2 mM TCEP, 5 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
4ETV Crystal structure of mouse ryanodine receptor 2 (2699-2904) Deposited 2012-04-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2699–2904（206 aa）	Mutation：K2879A Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；295 K；9% PEG3350, 0.1M Bicine, pH 9, vapor diffusion, hanging drop, temperature 295K	Resolution 1.65 Å R-free 0.250
4ETV Crystal structure of mouse ryanodine receptor 2 (2699-2904) Deposited 2012-04-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2699–2904（206 aa）	Mutation：K2879A Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；295 K；9% PEG3350, 0.1M Bicine, pH 9, vapor diffusion, hanging drop, temperature 295K	Resolution 1.65 Å R-free 0.250
4ETV Crystal structure of mouse ryanodine receptor 2 (2699-2904) Deposited 2012-04-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2699–2904（206 aa） Chain B 2699–2904（206 aa）	Mutation：K2879A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：K2879A Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；295 K；9% PEG3350, 0.1M Bicine, pH 9, vapor diffusion, hanging drop, temperature 295K	Resolution 1.65 Å R-free 0.250
4KEI Crystal structure of mouse Ryanodine Receptor 2 (1-217) disease mutant P164S Deposited 2013-04-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–217（217 aa） Fragment：N-terminal domain (UNP residues 1-217)	Mutation：P164S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；294 K；0.2 M sodium malonate, 5-15% saturated ammonium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K	Resolution 2.41 Å R-free 0.273
4KEJ Crystal structure of mouse Ryanodine Receptor 2 (1-217) disease mutant R169Q Deposited 2013-04-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–217（217 aa） Fragment：N-terminal domain (UNP residues 1-217)	Mutation：R169Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；294 K；0.2 M sodium malonate, 5-15% saturated ammonium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K	Resolution 2.55 Å R-free 0.297
4KEK Crystal structure of mouse Ryanodine Receptor 2 (1-217) disease mutant R176Q Deposited 2013-04-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–217（217 aa） Fragment：N-terminal domain (UNP residues 1-217)	Mutation：R176Q	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；294 K；0.2 M sodium malonate, 5-15% saturated ammonium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K	Resolution 2.15 Å R-free 0.290
4L4I Crystal structure of mouse Ryanodine Receptor isoform 2 (RyR2) 1-547 disease mutant R420Q Deposited 2013-06-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–547（547 aa） Fragment：N-terminal domains (UNP residues 1-547)	Mutation：R420Q	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；0.1 M Tris, pH 8.15, 5-10% PEG3350, 1% ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K	Resolution 2.15 Å R-free 0.263
4P9I Crystal Structure of mouse Ryanodine Receptor 2 SPRY2 Domain (1080-1253) Deposited 2014-04-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1080–1253（174 aa） Fragment：UNP residues 1080-1253	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298.15 K；sodium formate, peg 3350	Resolution 1.34 Å R-free 0.163
4P9I Crystal Structure of mouse Ryanodine Receptor 2 SPRY2 Domain (1080-1253) Deposited 2014-04-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1080–1253（174 aa） Fragment：UNP residues 1080-1253	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298.15 K；sodium formate, peg 3350	Resolution 1.34 Å R-free 0.163
4P9L Crystal Structure of mouse Ryanodine Receptor 2 SPRY2 Domain (1080-1253) disease mutant A1107M Deposited 2014-04-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1080–1253（174 aa） Fragment：UNP Residues 1080-1253	Mutation：A1107M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298.15 K；sodium formate, peg 3350	Resolution 1.44 Å R-free 0.184
4P9L Crystal Structure of mouse Ryanodine Receptor 2 SPRY2 Domain (1080-1253) disease mutant A1107M Deposited 2014-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1080–1253（174 aa） Fragment：UNP Residues 1080-1253	Mutation：A1107M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298.15 K；sodium formate, peg 3350	Resolution 1.44 Å R-free 0.184
5C33 Crystal Structure of Mouse Ryanodine Receptor 2 SPRY1 Domain Deposited 2015-06-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 650–844（195 aa） Fragment：SPRY1 domain (UNP residues 650-844)	Non-standard monomer：Yes (specific site not provided by mmCIF)	IPA ISOPROPYL ALCOHOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；0.1 M sodium acetate, pH 5.0, 0.6-0.9 M sodium sulfate	Resolution 1.21 Å R-free 0.172
5C33 Crystal Structure of Mouse Ryanodine Receptor 2 SPRY1 Domain Deposited 2015-06-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 650–844（195 aa） Fragment：SPRY1 domain (UNP residues 650-844)	Non-standard monomer：Yes (specific site not provided by mmCIF)	IPA ISOPROPYL ALCOHOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；0.1 M sodium acetate, pH 5.0, 0.6-0.9 M sodium sulfate	Resolution 1.21 Å R-free 0.172
5VSN Crystal structure of mouse ryanodine receptor 2 SPRY2 domain (1080-1253) disease mutant P1124L Deposited 2017-05-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1084–1252（169 aa） Fragment：SPRY2 domain (UNP residues 1084-1252)	Mutation：P1124L	GOL GLYCEROL × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M potassium thiocyanate, 30% PEG2000 MME	Resolution 1.44 Å R-free 0.193
6J6L Crystal structure of mouse Ryanodine Receptor 2 SPRY1 Domain (650-844) disease mutant I784F Deposited 2019-01-15	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 650–844（195 aa） Chain B 650–844（195 aa）	Mutation：I784F Mutation：I784F	IPA ISOPROPYL ALCOHOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M sodium acetate (PH4.5), 0.8 M sodium sulphate.	Resolution 1.45 Å R-free 0.204
6MM5 Catalytic subunit of cAMP-dependent protein kinase A in complex with RyR2 peptide (2799-2810) Deposited 2018-09-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2799–2810（12 aa） Fragment：residues 2799-2810	Not recorded	MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2M trimethylamine N-oxide, 0.1 M tris-HCl, 20% (w/v) PEG monomethyl ether 2K 25% (v/V) ethylene glycol	Resolution 1.95 Å R-free 0.227
6MM6 Catalytic subunit of cAMP-dependent protein kinase A in complex with RyR2 phosphorylation domain (2699-2904) Deposited 2018-09-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 2699–2904（206 aa） Fragment：residues 2699-2904	Mutation：K2879A	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.05M HEPES, 0.05 M KCl, 0.01M MgCl2, 15% (w/v) PEG 6K, and 25% (v/v) ethylene glycol	Resolution 2.39 Å R-free 0.261
6MM6 Catalytic subunit of cAMP-dependent protein kinase A in complex with RyR2 phosphorylation domain (2699-2904) Deposited 2018-09-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 2699–2904（206 aa） Fragment：residues 2699-2904	Mutation：K2879A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.05M HEPES, 0.05 M KCl, 0.01M MgCl2, 15% (w/v) PEG 6K, and 25% (v/v) ethylene glycol	Resolution 2.39 Å R-free 0.261
6MM7 Catalytic subunit of cAMP-dependent protein kinase A in complex with RyR2 K2879A, S2813D phosphomimetic (2699-2904) crystal form 1 Deposited 2018-09-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 2699–2904（206 aa） Fragment：residues 2699-2904	Mutation：K2879A, S2813D	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M magnesium formate and 25% (w/v) PEG 3350; 0.05 M HEPES, and 25% ethylene glycol	Resolution 1.85 Å R-free 0.238
6MM7 Catalytic subunit of cAMP-dependent protein kinase A in complex with RyR2 K2879A, S2813D phosphomimetic (2699-2904) crystal form 1 Deposited 2018-09-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 2699–2904（206 aa） Fragment：residues 2699-2904	Mutation：K2879A, S2813D	EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M magnesium formate and 25% (w/v) PEG 3350; 0.05 M HEPES, and 25% ethylene glycol	Resolution 1.85 Å R-free 0.238
6MM8 Catalytic subunit of cAMP-dependent protein kinase A in complex with RyR2 K2879A, S2813D phosphomimetic (2699-2904) crystal form 2 Deposited 2018-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2699–2904（206 aa） Fragment：residues 2699-2904	Mutation：K2879A, S2813D	PEG DI(HYDROXYETHYL)ETHER × 1 ACY ACETIC ACID × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 EDO 1,2-ETHANEDIOL × 5 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.15 M HEPES pH 7.5, 15% (w/v) PEG 20k, and 25% (v/v) ethylene glycol	Resolution 1.85 Å R-free 0.221
6WOU Cryo-EM structure of recombinant mouse Ryanodine Receptor type 2 mutant R176Q in complex with FKBP12.6 in nanodisc Deposited 2020-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–4966（4966 aa） Chain B 1–4966（4966 aa） Chain C 1–4966（4966 aa） Chain D 1–4966（4966 aa）	Mutation：R176Q Mutation：R176Q Mutation：R176Q Mutation：R176Q	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.27 Å
6WOV Cryo-EM structure of recombinant mouse Ryanodine Receptor type 2 wild type in complex with FKBP12.6 Deposited 2020-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–4966（4966 aa） Chain B 1–4966（4966 aa） Chain C 1–4966（4966 aa） Chain D 1–4966（4966 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.10 Å
6Y4O Calmodulin bound to cardiac ryanodine receptor (RyR2) calmodulin binding domain Deposited 2020-02-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 3580–3606（27 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298.15 K；0.1 M Sodium Acetate pH 4.70 and 23 % PEG 550 MME	Resolution 1.84 Å R-free 0.208
6Y4P Calmodulin N53I variant bound to cardiac ryanodine receptor (RyR2) calmodulin binding domain Deposited 2020-02-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 3580–3606（27 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298.15 K；0.1 M Sodium Acetate pH 4.70 and 23 % PEG 550 MME	Resolution 2.13 Å R-free 0.246
7VML Structure of recombinant RyR2 (EGTA dataset, class 1&2, closed state) Deposited 2021-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–1311（1311 aa） Chain A 1340–1386（47 aa） Chain A 1566–2507（942 aa） Chain A 2712–2915（204 aa） Chain A 3611–4966（1356 aa） Chain B 1–1311（1311 aa） Chain B 1340–1386（47 aa） Chain B 1566–2507（942 aa） Chain B 2712–2915（204 aa） Chain B 3611–4966（1356 aa） Chain C 1–1311（1311 aa） Chain C 1340–1386（47 aa） Chain C 1566–2507（942 aa） Chain C 2712–2915（204 aa） Chain C 3611–4966（1356 aa） Chain D 1–1311（1311 aa） Chain D 1340–1386（47 aa） Chain D 1566–2507（942 aa） Chain D 2712–2915（204 aa） Chain D 3611–4966（1356 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7VMM Structure of recombinant RyR2 (EGTA dataset, class 1, closed state) Deposited 2021-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–1311（1311 aa） Chain A 1340–1386（47 aa） Chain A 1566–2507（942 aa） Chain A 2712–2915（204 aa） Chain A 3611–4966（1356 aa） Chain B 1–1311（1311 aa） Chain B 1340–1386（47 aa） Chain B 1566–2507（942 aa） Chain B 2712–2915（204 aa） Chain B 3611–4966（1356 aa） Chain C 1–1311（1311 aa） Chain C 1340–1386（47 aa） Chain C 1566–2507（942 aa） Chain C 2712–2915（204 aa） Chain C 3611–4966（1356 aa） Chain D 1–1311（1311 aa） Chain D 1340–1386（47 aa） Chain D 1566–2507（942 aa） Chain D 2712–2915（204 aa） Chain D 3611–4966（1356 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7VMN Structure of recombinant RyR2 (EGTA dataset, class 2, closed state) Deposited 2021-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–1311（1311 aa） Chain A 1340–1386（47 aa） Chain A 1566–2507（942 aa） Chain A 2712–2915（204 aa） Chain A 3611–4966（1356 aa） Chain B 1–1311（1311 aa） Chain B 1340–1386（47 aa） Chain B 1566–2507（942 aa） Chain B 2712–2915（204 aa） Chain B 3611–4966（1356 aa） Chain C 1–1311（1311 aa） Chain C 1340–1386（47 aa） Chain C 1566–2507（942 aa） Chain C 2712–2915（204 aa） Chain C 3611–4966（1356 aa） Chain D 1–1311（1311 aa） Chain D 1340–1386（47 aa） Chain D 1566–2507（942 aa） Chain D 2712–2915（204 aa） Chain D 3611–4966（1356 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7VMO Structure of recombinant RyR2 (Ca2+ dataset, class 1, open state) Deposited 2021-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–1311（1311 aa） Chain A 1340–1386（47 aa） Chain A 1566–2507（942 aa） Chain A 2712–2915（204 aa） Chain A 3611–4966（1356 aa） Chain B 1–1311（1311 aa） Chain B 1340–1386（47 aa） Chain B 1566–2507（942 aa） Chain B 2712–2915（204 aa） Chain B 3611–4966（1356 aa） Chain C 1–1311（1311 aa） Chain C 1340–1386（47 aa） Chain C 1566–2507（942 aa） Chain C 2712–2915（204 aa） Chain C 3611–4966（1356 aa） Chain D 1–1311（1311 aa） Chain D 1340–1386（47 aa） Chain D 1566–2507（942 aa） Chain D 2712–2915（204 aa） Chain D 3611–4966（1356 aa）	Not recorded	ZN ZINC ION × 4 CA CALCIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7VMP Structure of recombinant RyR2 (Ca2+ dataset, class 2, open state) Deposited 2021-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–1311（1311 aa） Chain A 1340–1386（47 aa） Chain A 1566–2507（942 aa） Chain A 2712–2915（204 aa） Chain A 3611–4966（1356 aa） Chain B 1–1311（1311 aa） Chain B 1340–1386（47 aa） Chain B 1566–2507（942 aa） Chain B 2712–2915（204 aa） Chain B 3611–4966（1356 aa） Chain C 1–1311（1311 aa） Chain C 1340–1386（47 aa） Chain C 1566–2507（942 aa） Chain C 2712–2915（204 aa） Chain C 3611–4966（1356 aa） Chain D 1–1311（1311 aa） Chain D 1340–1386（47 aa） Chain D 1566–2507（942 aa） Chain D 2712–2915（204 aa） Chain D 3611–4966（1356 aa）	Not recorded	ZN ZINC ION × 4 CA CALCIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7VMQ Structure of recombinant RyR2 (Ca2+ dataset, class 3, open state) Deposited 2021-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–1311（1311 aa） Chain A 1340–1386（47 aa） Chain A 1566–2507（942 aa） Chain A 2712–2915（204 aa） Chain A 3611–4966（1356 aa） Chain B 1–1311（1311 aa） Chain B 1340–1386（47 aa） Chain B 1566–2507（942 aa） Chain B 2712–2915（204 aa） Chain B 3611–4966（1356 aa） Chain C 1–1311（1311 aa） Chain C 1340–1386（47 aa） Chain C 1566–2507（942 aa） Chain C 2712–2915（204 aa） Chain C 3611–4966（1356 aa） Chain D 1–1311（1311 aa） Chain D 1340–1386（47 aa） Chain D 1566–2507（942 aa） Chain D 2712–2915（204 aa） Chain D 3611–4966（1356 aa）	Not recorded	ZN ZINC ION × 4 CA CALCIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
7VMR Structure of recombinant RyR2 mutant K4593A (EGTA dataset) Deposited 2021-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–1311（1311 aa） Chain A 1340–1386（47 aa） Chain A 1566–2507（942 aa） Chain A 2712–2915（204 aa） Chain A 3611–4966（1356 aa） Chain B 1–1311（1311 aa） Chain B 1340–1386（47 aa） Chain B 1566–2507（942 aa） Chain B 2712–2915（204 aa） Chain B 3611–4966（1356 aa） Chain C 1–1311（1311 aa） Chain C 1340–1386（47 aa） Chain C 1566–2507（942 aa） Chain C 2712–2915（204 aa） Chain C 3611–4966（1356 aa） Chain D 1–1311（1311 aa） Chain D 1340–1386（47 aa） Chain D 1566–2507（942 aa） Chain D 2712–2915（204 aa） Chain D 3611–4966（1356 aa）	Mutation：K4593 Mutation：K4593 Mutation：K4593 Mutation：K4593 Mutation：K4593 Mutation：K4593 Mutation：K4593 Mutation：K4593 Mutation：K4593 Mutation：K4593 Mutation：K4593 Mutation：K4593 Mutation：K4593 Mutation：K4593 Mutation：K4593 Mutation：K4593 Mutation：K4593 Mutation：K4593 Mutation：K4593 Mutation：K4593	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7VMS Structure of recombinant RyR2 mutant K4593A (Ca2+ dataset) Deposited 2021-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–1311（1311 aa） Chain A 1340–1386（47 aa） Chain A 1566–2507（942 aa） Chain A 2712–2915（204 aa） Chain A 3611–4966（1356 aa） Chain B 1–1311（1311 aa） Chain B 1340–1386（47 aa） Chain B 1566–2507（942 aa） Chain B 2712–2915（204 aa） Chain B 3611–4966（1356 aa） Chain C 1–1311（1311 aa） Chain C 1340–1386（47 aa） Chain C 1566–2507（942 aa） Chain C 2712–2915（204 aa） Chain C 3611–4966（1356 aa） Chain D 1–1311（1311 aa） Chain D 1340–1386（47 aa） Chain D 1566–2507（942 aa） Chain D 2712–2915（204 aa） Chain D 3611–4966（1356 aa）	Mutation：K4593A Mutation：K4593A Mutation：K4593A Mutation：K4593A Mutation：K4593A Mutation：K4593A Mutation：K4593A Mutation：K4593A Mutation：K4593A Mutation：K4593A Mutation：K4593A Mutation：K4593A Mutation：K4593A Mutation：K4593A Mutation：K4593A Mutation：K4593A Mutation：K4593A Mutation：K4593A Mutation：K4593A Mutation：K4593A	ZN ZINC ION × 4 CA CALCIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8DTY Recombinant mouse RyR2 triple phosphomimetic mutant S2807D/S2813D/S2030D in complex with FKBP12.6 and nanodisc under closed-state conditions Deposited 2022-07-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–4966（4966 aa） Chain B 1–4966（4966 aa） Chain C 1–4966（4966 aa） Chain D 1–4966（4966 aa）	Mutation：S2807D, S2813D, S2030D Mutation：S2807D, S2813D, S2030D Mutation：S2807D, S2813D, S2030D Mutation：S2807D, S2813D, S2030D	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8DTZ Recombinant mouse RyR2 triple phosphonull mutant S2807A/S2813A/S2030A in complex with FKBP12.6 and nanodisc under closed-state conditions Deposited 2022-07-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–4966（4966 aa） Chain B 1–4966（4966 aa） Chain C 1–4966（4966 aa） Chain D 1–4966（4966 aa）	Mutation：S2807A, S2813A, S2030A Mutation：S2807A, S2813A, S2030A Mutation：S2807A, S2813A, S2030A Mutation：S2807A, S2813A, S2030A	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8DVV Recombinant mouse RyR2 triple phosphomimetic mutant S2807D/S2813D/S2030D in complex with FKBP12.6 and nanodisc under open-state conditions Deposited 2022-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–4966（4966 aa） Chain B 1–4966（4966 aa） Chain C 1–4966（4966 aa） Chain D 1–4966（4966 aa）	Mutation：S2807D, S2813D, S2030D Mutation：S2807D, S2813D, S2030D Mutation：S2807D, S2813D, S2030D Mutation：S2807D, S2813D, S2030D	CA CALCIUM ION × 4 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.68 Å
8RRS Structure of mouse RyR2 solubilised in detergent in open state in complex with Ca2+, ATP, caffeine and Nb9657. Deposited 2024-01-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–4966（4966 aa） Chain C 1–4966（4966 aa） Chain E 1–4966（4966 aa） Chain F 1–4966（4966 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 CFF CAFFEINE × 4 ZN ZINC ION × 4 CA CALCIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

31 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RYR2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–547； UniProt 1–547

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4l4h
Deposition date deposition_date	2013-06-07
Structure title title	Crystal structure of mouse Ryanodine Receptor isoform 2 (RyR2) 1-547
Keywords keywords	Ca2+ release, ion channel, ER/SR Membrane, METAL TRANSPORT; METAL TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	24.38 Å
Radius of gyration Rg (electron density) rg_electron	23.37 Å
Forward intensity I(0) i0	44332700.00
Molecular weight molecular_weight	50506.0 kDa
Excluded volume excluded_volume	62760 Å³
Envelope volume envelope_volume	76397 Å³
Hydration-shell volume shell_volume	27021 Å³
Envelope diameter envelope_diameter	76.7 Å
Shell Rg shell_rg	30.61 Å
Envelope Rg envelope_rg	23.52 Å
Shape Rg shape_rg	23.40 Å
Total Rg total_rg	24.11 Å
Total atoms total_atoms	3556
Residues n_residues	466
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

▼

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

Maximum dimension Dmax dmax	74.8 Å
Rg (real space) rg_real	24.25 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	4.4330e+07
I(0) uncertainty (real space) i0_real_error	5.3590e+05
Rg (reciprocal space) rg_reciprocal	24.28 Å
I(0) (reciprocal space) i0_reciprocal	44330000.0000
Solution quality estimate total_estimate	0.9035
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.5 Å
Skewness Skewness skewness	0.167
Kurtosis Kurtosis kurtosis	-0.534
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7259000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.887

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Ryanodine receptor 2
Molecular weight formula_weight	61578.6 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	3665

MADAGEGEDEIQFLRTDDEVVLQCTATIHKEQQKLCLAAEGFGNRLCFLESTSNSKNVPPDLSICTFVLEQSLSVRALQEMLANTVEKSEGQVDVEKWKFMMKTAQGGGHRTLLYGHAILLRHSYSGMYLCCLSTSRSSTDKLAFDVGLQEDTTGEACWWTIHPASKQRSEGEKVRVGDDLILVSVSSERYLHLSYGNSSWHVDAAFQQTLWSVAPISSGSEAAQGYLIGGDVLRLLHGHMDECLTVPSGEHGEEQRRTVHYEGGAVSVHARSLWRLETLRVAWSGSHIRWGQPFRLRHVTTGKYLSLMEDKNLLLMDKEKADVKSTAFAFRSSKEKLDVGVRKEVDGMGTSEIKYGDSICYIQHVDTGLWLTYQAVDVKSARMGSIQRKAIMHHEGHMDDGLNLSRSQHEESRTARVIRSTVFLFNRFIRGLDALSKKVKLPTIDLPIESVSLSLQDLIGYFHPPDEHLEHEDKQNRLRALKNRQNLFQEEGMINLVLECIDRLHVYSSAAHFADVAGREAGESWKSILNSLYELLAALIRGNRKN

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	82

▼

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	4l4hA01
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4l4hA02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	4l4hA03
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	30 — IP3 receptor type 1 binding core, RIH domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	78.040 Å
Unit-cell length b length_b	78.040 Å
Unit-cell length c length_c	248.380 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	8

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	48.710 Å
R factor r_factor	0.2218
R_work r_work	0.2203
R_free r_free	0.2511

fit	/app/data/saxs_computation/l4/4l4h/4l4h.fit
pddf	/app/data/pr_computation/l4/4l4h/4l4h.pr.out
profile	/app/data/saxs_computation/l4/4l4h/4l4h.dat