9vlg

Structure of human alpha-2/delta-1 with crisugabalin

Method: ELECTRON MICROSCOPY D_max: 108.4 Å Quality: GOOD

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

Isoform 2 of Voltage-dependent calcium channel subunit alpha-2/delta-1

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	Other combination Monomer Protein × 1 其他Polymer 4 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 25–1064	Not recorded	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 A1ESQ Crisugabalin × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.01 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 9VLG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7MIX Human N-type voltage-gated calcium channel Cav2.2 in the presence of ziconotide at 3.0 Angstrom resolution Deposited 2021-04-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–1103（1103 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 2 Y01 CHOLESTEROL HEMISUCCINATE × 2 CLR CHOLESTEROL × 5 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2 PT5 [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；blot for 6 seconds before plunging	Resolution 3.00 Å
7MIY Human N-type voltage-gated calcium channel Cav2.2 at 3.1 Angstrom resolution Deposited 2021-04-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–1103（1103 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 2 Y01 CHOLESTEROL HEMISUCCINATE × 3 CLR CHOLESTEROL × 4 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2 PT5 [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；blot for 6 seconds before plunging	Resolution 3.10 Å
7UHF Human L-type voltage-gated calcium channel Cav1.3 in the presence of cinnarizine at 3.1 Angstrom resolution Deposited 2022-03-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–1103（1103 aa）	Not recorded	N90 1-(diphenylmethyl)-4-[(2E)-3-phenylprop-2-en-1-yl]piperazine × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 2 Y01 CHOLESTEROL HEMISUCCINATE × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7UHG Human L-type voltage-gated calcium channel Cav1.3 at 3.0 Angstrom resolution Deposited 2022-03-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–1103（1103 aa）	Not recorded	CA CALCIUM ION × 2 CLR CHOLESTEROL × 3 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7VFS Human N-type voltage gated calcium channel CaV2.2-alpha2/delta1-beta1 complex, apo state Deposited 2021-09-13	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–1103（1103 aa）	Not recorded	R16 HEXADECANE × 18 Y01 CHOLESTEROL HEMISUCCINATE × 3 PT5 [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate × 1 CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7VFU Human N-type voltage gated calcium channel CaV2.2-alpha2/delta1-beta1 complex, bound to ziconotide Deposited 2021-09-13	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–1103（1103 aa）	Not recorded	R16 HEXADECANE × 18 Y01 CHOLESTEROL HEMISUCCINATE × 3 PT5 [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate × 1 CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7VFV Human N-type voltage gated calcium channel CaV2.2-alpha2/delta1-beta1 complex, bound to PD173212 Deposited 2021-09-13	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–1103（1103 aa）	Not recorded	R16 HEXADECANE × 16 Y01 CHOLESTEROL HEMISUCCINATE × 3 PT5 [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate × 1 6IX (2~{S})-~{N}-[(2~{S})-1-(~{tert}-butylamino)-1-oxidanylidene-3-(4-phenylmethoxyphenyl)propan-2-yl]-2-[(4-~{tert}-butylphenyl)methyl-methyl-amino]-4-methyl-pentanamide × 1 CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7VFW Human N-type voltage gated calcium channel CaV2.2-alpha2/delta1-beta1 complex, bound to CaV2.2-blocker1 Deposited 2021-09-13	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–1103（1103 aa）	Not recorded	R16 HEXADECANE × 15 Y01 CHOLESTEROL HEMISUCCINATE × 3 PT5 [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate × 1 6I7 5-(4-chlorophenyl)-1-(2-methoxyphenyl)-3-(2,2,6,6-tetramethyloxan-4-yl)pyrazole × 1 CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7XLQ Structure of human R-type voltage-gated CaV2.3-alpha2/delta1-beta1 channel complex in the ligand-free (apo) state Deposited 2022-04-22	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 27–1103（1077 aa）	Not recorded	Y01 CHOLESTEROL HEMISUCCINATE × 6 R16 HEXADECANE × 7 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1 CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7YG5 Structure of human R-type voltage-gated CaV2.3-alpha2/delta1-beta1 channel complex in the topiramate-bound state Deposited 2022-07-11	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–1103（1103 aa）	Not recorded	Y01 CHOLESTEROL HEMISUCCINATE × 9 R16 HEXADECANE × 6 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2 CA CALCIUM ION × 2 TOR [(3aS,5aR,8aR,8bS)-2,2,7,7-tetramethyltetrahydro-3aH-bis[1,3]dioxolo[4,5-b:4',5'-d]pyran-3a-yl]methyl sulfamate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8E59 Human L-type voltage-gated calcium channel Cav1.3 in the presence of Amiodarone at 3.1 Angstrom resolution Deposited 2022-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–1103（1103 aa）	Not recorded	BBI (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone × 1 CA CALCIUM ION × 2 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8E5A Human L-type voltage-gated calcium channel Cav1.3 treated with 1.4 mM Sofosbuvir at 3.3 Angstrom resolution Deposited 2022-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–1103（1103 aa）	Not recorded	CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8E5B Human L-type voltage-gated calcium channel Cav1.3 in the presence of Amiodarone and Sofosbuvir at 3.3 Angstrom resolution Deposited 2022-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–1103（1103 aa）	Not recorded	BBI (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone × 1 WG6 Sofosbuvir × 1 CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8EPL Human R-type voltage-gated calcium channel Cav2.3 at 3.1 Angstrom resolution Deposited 2022-10-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–1103（1103 aa）	Not recorded	CA CALCIUM ION × 2 CLR CHOLESTEROL × 5 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2 PT5 [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8EPM Human R-type voltage-gated calcium channel Cav2.3 CH2II-deleted mutant at 3.1 Angstrom resolution Deposited 2022-10-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–1103（1103 aa）	Not recorded	CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8FHS Human L-type voltage-gated calcium channel Cav1.2 in the presence of amiodarone and sofosbuvir at 3.3 Angstrom resolution Deposited 2022-12-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–1103（1103 aa）	Not recorded	CA CALCIUM ION × 2 BBI (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone × 1 WG6 Sofosbuvir × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2 CLR CHOLESTEROL × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8HLP Cryo-EM structure of human high-voltage activated L-type calcium channel CaV1.2 (apo) Deposited 2022-11-30	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–1071（1071 aa）	Not recorded	R16 HEXADECANE × 9 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2 CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8HMA Cryo-EM structure of human high-voltage activated L-type calcium channel CaV1.2 in complex with tetrandrine (TET) Deposited 2022-12-02	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–1071（1071 aa）	Not recorded	R16 HEXADECANE × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 3 A1AC9 6,6',7,12-tetramethoxy-2,2'-dimethyl-1beta-3,4-didehydroberbaman × 1 CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11 BMA beta-D-mannopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8HMB Cryo-EM structure of human high-voltage activated L-type calcium channel CaV1.2 in complex with benidipine (BEN) Deposited 2022-12-02	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–1071（1071 aa）	Not recorded	R16 HEXADECANE × 8 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 3 A1AC8 (3R)-1-benzylpiperidin-3-yl methyl (4R)-2,6-dimethyl-4-(3-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylate × 1 CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8IF3 Structure of human alpha-2/delta-1 with mirogabalin Deposited 2023-02-17	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1091（1091 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 8X9 2-[(1R,5S,6S)-6-(aminomethyl)-3-ethyl-6-bicyclo[3.2.0]hept-3-enyl]acetic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.23 Å
8IF4 Structure of human alpha-2/delta-1 without mirogabalin Deposited 2023-02-17	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1091（1091 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.23 Å
8WE6 Human L-type voltage-gated calcium channel Cav1.2 at 2.9 Angstrom resolution Deposited 2023-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–1103（1103 aa）	Not recorded	CA CALCIUM ION × 2 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1 CLR CHOLESTEROL × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PT5 [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8WE7 Human L-type voltage-gated calcium channel Cav1.2 in the presence of calciseptine at 3.2 Angstrom resolution Deposited 2023-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–1103（1103 aa）	Not recorded	CA CALCIUM ION × 2 CLR CHOLESTEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8WE8 Human L-type voltage-gated calcium channel Cav1.2 in the presence of calciseptine, amlodipine and pinaverium at 2.9 Angstrom resolution Deposited 2023-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–1103（1103 aa）	Not recorded	CA CALCIUM ION × 2 CLR CHOLESTEROL × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PT5 [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate × 1 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1 6UB amlodipine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8WE9 Human L-type voltage-gated calcium channel Cav1.2 (Class I) in the presence of pinaverium at 3.0 Angstrom resolution Deposited 2023-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–1103（1103 aa）	Not recorded	CA CALCIUM ION × 2 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1 CLR CHOLESTEROL × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PT5 [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8WEA Human L-type voltage-gated calcium channel Cav1.2 (Class II) in the presence of pinaverium at 3.2 Angstrom resolution Deposited 2023-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–1103（1103 aa）	Not recorded	CA CALCIUM ION × 2 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 WB9 4-[(2-bromanyl-4,5-dimethoxy-phenyl)methyl]-4-[2-[2-[(1~{R},2~{S},5~{R})-6,6-dimethyl-2-bicyclo[3.1.1]heptanyl]ethoxy]ethyl]morpholin-4-ium × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8X90 P/Q type calcium channel Deposited 2023-11-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–1103（1103 aa）	Not recorded	PS1 1,2-DIDECANOYL-SN-GLYCERO-3-[PHOSPHO-L-SERINE] × 1 CLR CHOLESTEROL × 5 PT5 [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate × 1 CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 Y01 CHOLESTEROL HEMISUCCINATE × 3 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å
8X91 P/Q type calcium channel in complex with omega-conotoxin MVIIC Deposited 2023-11-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–1103（1103 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 3 CLR CHOLESTEROL × 5 PT5 [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate × 1 Y01 CHOLESTEROL HEMISUCCINATE × 3 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.11 Å
8X93 P/Q type calcium channel in complex with omega-Agatoxin IVA Deposited 2023-11-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–1103（1103 aa）	Not recorded	CA CALCIUM ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CLR CHOLESTEROL × 5 PT5 [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate × 1 Y01 CHOLESTEROL HEMISUCCINATE × 3 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.92 Å

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

View Construct and Data Evidence

UniProt name	CA2D1_HUMAN
Isoform	P54289-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 17–1064； UniProt 25–1064

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	9vlg
Deposition date deposition_date	2025-06-25
Structure title title	Structure of human alpha-2/delta-1 with crisugabalin
Keywords keywords	Complex, Alpha-2/delta-1, Crisugabalin, 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	33.59 Å
Radius of gyration Rg (electron density) rg_electron	33.11 Å
Forward intensity I(0) i0	337801000.00
Molecular weight molecular_weight	99014.0 kDa
Excluded volume excluded_volume	95857 Å³
Envelope volume envelope_volume	168080 Å³
Hydration-shell volume shell_volume	42770 Å³
Envelope diameter envelope_diameter	111.0 Å
Shell Rg shell_rg	39.70 Å
Envelope Rg envelope_rg	32.64 Å
Shape Rg shape_rg	33.04 Å
Total Rg total_rg	33.58 Å
Total atoms total_atoms	7511
Residues n_residues	910
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	108.4 Å
Rg (real space) rg_real	33.59 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	3.3780e+08
I(0) uncertainty (real space) i0_real_error	4.8080e+06
Rg (reciprocal space) rg_reciprocal	33.59 Å
I(0) (reciprocal space) i0_reciprocal	337800000.0000
Solution quality estimate total_estimate	0.8983
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.9 Å
Skewness Skewness skewness	0.300
Kurtosis Kurtosis kurtosis	-0.577
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	69000000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.939

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Isoform 2 of Voltage-dependent calcium channel subunit alpha-2/delta-1
Molecular weight formula_weight	120990.8 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	7511

HHHHHHHHWSHPQFEKEPFPSAVTIKSWVDKMQEDLVTLAKTASGVNQLVDIYEKYQDLYTVEPNNARQLVEIAARDIEKLLSNRSKALVRLALEAEKVQAAHQWREDFASNEVVYYNAKDDLDPEKNDSEPGSQRIKPVFIEDANFGRQISYQHAAVHIPTDIYEGSTIVLNELNWTSALDEVFKKNREEDPSLLWQVFGSATGLARYYPASPWVDNSRTPNKIDLYDVRRRPWYIQGAASPKDMLILVDVSGSVSGLTLKLIRTSVSEMLETLSDDDFVNVASFNSNAQDVSCFQHLVQANVRNKKVLKDAVNNITAKGITDYKKGFSFAFEQLLNYNVSRANCNKIIMLFTDGGEERAQEIFNKYNKDKKVRVFTFSVGQHNYDRGPIQWMACENKGYYYEIPSIGAIRINTQEYLDVLGRPMVLAGDKAKQVQWTNVYLDALELGLVITGTLPVFNITGQFENKTNLKNQLILGVMGVDVSLEDIKRLTPRFTLCPNGYYFAIDPNGYVLLHPNLQPKNPKSQEPVTLDFLDAELENDIKVEIRNKMIDGESGEKTFRTLVKSQDERYIDKGNRTYTWTPVNGTDYSLALVLPTYSFYYIKAKLEETITQARSKKGKMKDSETLKPDNFEESGYTFIAPRDYCNDLKISDNNTEFLLNFNEFIDRHHHHHHHHKTPNNPSCNADLINRVLLDAGFTNELVQNYWSKQKNIKGVKARFVVTDGGITRVYPKEAGENWQENPETYEDSFYKRSLDNDNYVFTAPYFNKSGPGAYESGIMVSKAVEIYIQGKLLKPAVVGIKIDVNSWIENFTKTSIRDPCAGPVCDCKRNSDVMDCVILDDGGFLLMANHDDYTNQIGRFFGEIDPSLMRHLVNISVYAFNKSYDYQSVCEPGAAPKQGAGHRSAYVPSVADILQIGWWATAAAWSILQQFLLSLTFPRLLEAVEMEDDDFTASLSKQSCITEQTQYFFDNDSKSFSGVLDCGNCSRIFHGEKLMNTNLIFIMVESKGTCPCDTRLLIQAEQTSDGPNPCDMVKQPRYRKGPDVCFDNNVLEDYTDCGGVSG

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	Homo sapiens

Entity 2 Entity 2 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	3

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	Crisugabalin
Molecular weight formula_weight	209.3 kDa
Source method src_method	syn
Copy count entity_count	1

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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	3.01 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	226483

fit	/app/data/saxs_computation/vl/9vlg/9vlg.fit
pddf	/app/data/pr_computation/vl/9vlg/9vlg.pr.out
profile	/app/data/saxs_computation/vl/9vlg/9vlg.dat