6mc9

Crystal Structure of Human Nav1.4 C-Terminal (1599-1754) domain in complex with calcium-bound calmodulin

Method: X-RAY DIFFRACTION D_max: 90.7 Å Quality: GOOD

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

Sodium channel protein type 4 subunit alpha

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1599–1754	Not recorded	Calmodulin-1 × 1 （P0DP29） CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；293 K；0.1M MES pH 6.0, 20% PEG 6000, 1.0M LiCl	Resolution 3.30 Å R-free 0.285

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 6MC9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6AGF Structure of the human voltage-gated sodium channel Nav1.4 in complex with beta1 Deposited 2018-08-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1836（1836 aa）	Not recorded	6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 6 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 5.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
6MBA Crystal Structure of Human Nav1.4 CTerminal Domain in Complex with apo Calmodulin Deposited 2018-08-29	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1599–1764（166 aa） Fragment：cytoplasmic domain	Not recorded	CL CHLORIDE ION × 4 EDO 1,2-ETHANEDIOL × 1 CO3 CARBONATE ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；0.1M MES pH 6.0, 20% PEG 6000, 1.0M LiCl	Resolution 1.80 Å R-free 0.234

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SCN4A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–161； UniProt 1599–1754

Calmodulin-1

Rattus norvegicus

UniProt P0DP29

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–149	Not recorded	Sodium channel protein type 4 subunit alpha × 1 （P35499） CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；293 K；0.1M MES pH 6.0, 20% PEG 6000, 1.0M LiCl	Resolution 3.30 Å R-free 0.285

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6MC9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3EK4 Calcium-saturated GCaMP2 Monomer Deposited 2008-09-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–149（147 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.1 M Magnesium formate dihydrate, 15% w/v Polyethylene glycol 3,350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.65 Å R-free 0.280
3EK7 Calcium-saturated GCaMP2 dimer Deposited 2008-09-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3–149（147 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.2 M lithium sulfate monohydrate, 0.1 M Tris-HCl pH 8.5, 30%(w/v) polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.85 Å R-free 0.241
3EK8 Calcium-saturated GCaMP2 T116V/G87R mutant monomer Deposited 2008-09-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–149（147 aa）	Mutation：T116V, G87R Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.1 M Magnesium formate dihydrate, 15% w/v Polyethylene glycol 3,350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.266
3EKH Calcium-saturated GCaMP2 T116V/K378W mutant monomer Deposited 2008-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–149（147 aa）	Mutation：T116V, K378W Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.1 M Magnesium formate dihydrate, 15% w/v Polyethylene glycol 3,350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.224
3EKJ Calcium-free GCaMP2 (calcium binding deficient mutant) Deposited 2008-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–149（147 aa）	Mutation：T329G, E334Q, D359G, E370Q, D396G, E407Q, D432G, E443Q 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 5.5；298 K；0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.280
3EVR Crystal structure of Calcium bound monomeric GCAMP2 Deposited 2008-10-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–148（146 aa） Fragment：UNP P42212 residues 2-238, UNP P0DP29 residues 148-305	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.190
3EVU Crystal structure of Calcium bound dimeric GCAMP2 Deposited 2008-10-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3–148（146 aa） Fragment：UNP P11799 residues 1731-1749, UNP P42212 residues 2-144/147-238, UNP P0DP29 residues 3-238	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.75 Å R-free 0.197
3SG2 Crystal Structure of GCaMP2-T116V,D381Y Deposited 2011-06-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–149（147 aa） Fragment：SEE REMARK 999	Mutation：T116V,D381Y Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M ammonium acetate, 0.1 M Tris, pH 8.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.207
3SG3 Crystal Structure of GCaMP3-D380Y Deposited 2011-06-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–149（147 aa） Fragment：SEE REMARK 999	Mutation：D380Y Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M sodium chloride, 0.1 M Tris, pH 8.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.10 Å R-free 0.199
3SG4 Crystal Structure of GCaMP3-D380Y, LP(linker 2) Deposited 2011-06-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–149（147 aa） Fragment：SEE REMARK 999	Mutation：D380Y, LP(linker 2) Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M sodium chloride, 0.1 M Tris, pH 8.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.40 Å R-free 0.213
3SG5 Crystal Structure of Dimeric GCaMP3-D380Y, QP(linker 1), LP(linker 2) Deposited 2011-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3–149（147 aa） Fragment：SEE REMARK 999	Mutation：D380Y, QP(linker 1), LP(linker 2) Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 8 SO4 SULFATE ION × 8 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M Bis-Tris, pH 6.5, 2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.226
3SG6 Crystal Structure of Dimeric GCaMP2-LIA(linker 1) Deposited 2011-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3–149（147 aa） Fragment：SEE REMARK 999	Mutation：LIA(linker 1) Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M lithium sulfate, 0.1 M Tris, pH 8.5, 30% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.70 Å R-free 0.249
3SG7 Crystal Structure of GCaMP3-KF(linker 1) Deposited 2011-06-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–149（147 aa） Fragment：SEE REMARK 999	Mutation：KF(linker 1) Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M ammonium sulfate, 0.1 M Tris, pH 8.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.230
3WLC Crystal structure of dimeric GCaMP6m Deposited 2013-11-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3–149（147 aa） Fragment：UNP RESIDUES 37-55, 149-238, 2-144, 3-149	Mutation：M153K, V163A, S175G, D180Y, T203V, A206K, H231L, F64L, V93I, N61D, D79Y, M77G, K78S, T80R, S82T, R91G Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M HEPES, 20% w/v PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.49 Å R-free 0.225
3WLD Crystal structure of monomeric GCaMP6m Deposited 2013-11-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–149（147 aa） Fragment：UNP RESIDUES 37-55, 149-238, 2-144, 3-149	Mutation：M153K, V163A, S175G, D180Y, T203V, A206K, H231L, F64L, V93I, N61D, D79Y, M77G, K78S, T80R, S82T, R91G Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.1M HEPES, 18% w/v PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.212
6CZQ A V-to-F substitution in SK2 channels causes Ca2+ hypersensitivity and improves locomotion in a C. elegans ALS model Deposited 2018-04-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain R 5–148（144 aa） Fragment：residues 5-148	Not recorded	SO4 SULFATE ION × 3 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293.15 K；0.1 M Sodium citrate tribasic dihydrate 0.5 M Ammonium sulfate 1.5 M Lithium sulfate monohydrate	Resolution 2.20 Å R-free 0.249
6DMW Calmodulin-bound full-length rbTRPV5 Deposited 2018-06-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–149（149 aa）	Not recorded	CA CALCIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
6MBA Crystal Structure of Human Nav1.4 CTerminal Domain in Complex with apo Calmodulin Deposited 2018-08-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–149（149 aa）	Not recorded	CL CHLORIDE ION × 4 EDO 1,2-ETHANEDIOL × 1 CO3 CARBONATE ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；0.1M MES pH 6.0, 20% PEG 6000, 1.0M LiCl	Resolution 1.80 Å R-free 0.234
7NQC Calmodulin extracts the Ras family protein RalA from lipid bilayers by engagement with two membrane targeting motifs Deposited 2021-03-01	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–149（149 aa）	Not recorded	CA CALCIUM ION × 4 ULW [(2~{Z},6~{Z})-3,7,11-trimethyldodeca-2,6-dienyl] 3-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]propanoate × 1	SOLUTION NMR NMR measurement conditions pH 6.7；298 K；Ionic strength (raw mmCIF value) 109；Pressure 1 NMR sample composition 0.8 mM [U-15N] Calmodulin, 0.8 mM NA RalA HVR, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.1 mM U-15N, 13C Calmodulin, 1.1 mM NA RalA HVR, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM Calmodulin, 1.0 mM 15N,13C RalA HVR, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
8V2G Cryo-EM structure of the KCa2.2 channel in apo state Deposited 2023-11-22	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 E 3–148（146 aa） Chain F 3–148（146 aa） Chain G 3–148（146 aa） Chain H 3–148（146 aa）	Not recorded	K POTASSIUM ION × 4 CA CALCIUM ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å
8V2H Cryo-EM structure of the KCa2.2 channel bound to inhibitor AP14145. Deposited 2023-11-22	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 E 3–148（146 aa） Chain F 3–148（146 aa） Chain G 3–148（146 aa） Chain H 3–148（146 aa）	Not recorded	K POTASSIUM ION × 4 CA CALCIUM ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8V3G Cryo-EM structure of the KCa2.2 channel with inhibitor UCL 1684. Deposited 2023-11-27	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 E 3–148（146 aa） Chain F 3–148（146 aa） Chain G 3–148（146 aa） Chain H 3–148（146 aa）	Not recorded	K POTASSIUM ION × 4 Y7Z UCL1684 × 1 CA CALCIUM ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9ED1 Cryo-EM structure of the human KCa3.1/calmodulin channel in complex with Ca2+ and 1,4-dihydropyridine (DHP-103) Deposited 2024-11-15	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 E 4–148（145 aa） Chain F 4–148（145 aa） Chain G 4–148（145 aa） Chain H 4–148（145 aa）	Not recorded	K POTASSIUM ION × 5 CA CALCIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9EIO Cryo-EM structure of the mutant KCa2.2_F244S channel Deposited 2024-11-26	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 E 4–145（142 aa） Chain F 4–145（142 aa） Chain G 4–145（142 aa） Chain H 4–145（142 aa）	Not recorded	K POTASSIUM ION × 4 CA CALCIUM ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å
9KYS the Ca2+/CaM-CASK-ARD complex Deposited 2024-12-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–149（149 aa） Chain C 1–149（149 aa）	Not recorded	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；magnesium chloride, PEG 3350	Resolution 1.76 Å R-free 0.231
9M5Y the crystal structure of the Ca2+/CaM-CASK-CaMK complex Deposited 2025-03-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–149（149 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 PO4 PHOSPHATE ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；0.1 M Sodium citrate tribasic dihydrate, pH 5.0, 10% (v/v) PEG 6000.	Resolution 1.80 Å R-free 0.197
9M6G the crystal structure of the Ca2+/CaM-CASK-CaMK-Mint1-CID complex Deposited 2025-03-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–149（149 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MLI MALONATE ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；289 K；0.1 M Sodium malonate, pH 5.0, 12% (v/v) PEG 3350	Resolution 1.70 Å R-free 0.187
9O7S Cryo-EM structure of KCa2.2/calmodulin channel in complex with NS309 Deposited 2025-04-15	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 E 4–148（145 aa） Chain F 4–148（145 aa） Chain G 4–148（145 aa） Chain H 4–148（145 aa）	Not recorded	K POTASSIUM ION × 3 1KP (3E)-6,7-dichloro-3-(hydroxyimino)-1,3-dihydro-2H-indol-2-one × 4 CA CALCIUM ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.71 Å
9O85 Cryo-EM structure of KCa2.2_I/calmodulin channel in complex with rimtuzalcap Deposited 2025-04-15	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 E 5–148（144 aa） Chain F 5–148（144 aa） Chain G 5–148（144 aa） Chain H 5–148（144 aa）	Not recorded	K POTASSIUM ION × 3 A1B92 Rimtuzalcap × 4 CA CALCIUM ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.13 Å
9O93 Cryo-EM structure of KCa2.2_II/calmodulin channel in complex with rimtuzalcap Deposited 2025-04-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 5–148（144 aa） Chain F 5–148（144 aa） Chain G 5–148（144 aa） Chain H 5–148（144 aa）	Not recorded	K POTASSIUM ION × 2 A1B92 Rimtuzalcap × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.96 Å
9OA8 Cryo-EM structure of KCa3.1/calmodulin channel in complex with NS309 Deposited 2025-04-19	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 E 3–148（146 aa） Chain F 3–148（146 aa） Chain G 3–148（146 aa） Chain H 3–148（146 aa）	Not recorded	K POTASSIUM ION × 3 1KP (3E)-6,7-dichloro-3-(hydroxyimino)-1,3-dihydro-2H-indol-2-one × 4 CA CALCIUM ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.59 Å
9U9D Bipartite Genetically Encoded Biosensor sG-GECO1 Deposited 2025-03-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 3–149（147 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2m sodium malonate dibasic monohydrate, 0.1M Bis-Tris propane pH 8.5, 20% w/v PEG 3350	Resolution 1.80 Å R-free 0.227

32 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CALM1_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–149； UniProt 1–149

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	6mc9
Deposition date deposition_date	2018-08-30
Structure title title	Crystal Structure of Human Nav1.4 C-Terminal (1599-1754) domain in complex with calcium-bound calmodulin
Keywords keywords	SCN4A, voltage gated sodium channel, calmodulin, calmodulin-binding protein, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	23.84 Å
Radius of gyration Rg (electron density) rg_electron	23.07 Å
Forward intensity I(0) i0	20140100.00
Molecular weight molecular_weight	33374.0 kDa
Excluded volume excluded_volume	41489 Å³
Envelope volume envelope_volume	54517 Å³
Hydration-shell volume shell_volume	21020 Å³
Envelope diameter envelope_diameter	94.1 Å
Shell Rg shell_rg	28.01 Å
Envelope Rg envelope_rg	23.16 Å
Shape Rg shape_rg	23.07 Å
Total Rg total_rg	23.71 Å
Total atoms total_atoms	2330
Residues n_residues	291
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	90.7 Å
Rg (real space) rg_real	23.90 Å
Rg uncertainty (real space) rg_real_error	1.10 Å
I(0) (real space) i0_real	2.0140e+07
I(0) uncertainty (real space) i0_real_error	3.4230e+05
Rg (reciprocal space) rg_reciprocal	23.89 Å
I(0) (reciprocal space) i0_reciprocal	20140000.0000
Solution quality estimate total_estimate	0.8111
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.5 Å
Skewness Skewness skewness	0.441
Kurtosis Kurtosis kurtosis	0.066
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3278000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.596; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.762; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Sodium channel protein type 4 subunit alpha
Molecular weight formula_weight	19211.9 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	2330

GPLGSENFNVATEESSEPLGEDDFEMFYETWEKFDPDATQFIAYSRLSDFVDTLQEPLRIAKPNKIKLITLDLPMVPGDKIHCLDILFALTKEVLGDSGEMDALKQTMEEKFMAANPSKVSYEPITTTLKRKHEEVCAIKIQRAYRRHLLQRSMKQASYMYLTRAAAS

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	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Calmodulin-1
Molecular weight formula_weight	16852.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli BL21

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6mc9B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

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8. Citations (1)

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Unit-cell length a length_a	72.615 Å
Unit-cell length b length_b	72.615 Å
Unit-cell length c length_c	134.661 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	40.829 Å
R factor r_factor	0.2421
R_work r_work	0.2400
R_free r_free	0.2853

fit	/app/data/saxs_computation/mc/6mc9/6mc9.fit
pddf	/app/data/pr_computation/mc/6mc9/6mc9.pr.out
profile	/app/data/saxs_computation/mc/6mc9/6mc9.dat

Crystal Structure of Human Nav1.4 C-Terminal (1599-1754) domain in complex with calcium-bound calmodulin

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

Sodium channel protein type 4 subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Calmodulin-1

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)