← Back to search
3rvz

Crystal structure of the NavAb voltage-gated sodium channel (Ile217Cys, 2.8 A)

Method: X-RAY DIFFRACTION Dmax: 93.0 Å Quality: EXCELLENT
▼

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

Ion transport protein

Arcobacter butzleri

UniProt A8EVM5

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–267 Chain B； UniProt 1–267 Mutation：I217C PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 28 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.75；298 K；CHAPSO:DMPC bicelles, 2 M ammonium sulphate, 0.1 M Na-citrate pH 4.75, 28% glucose, nicotinic acid (sat.), VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.80 Å R-free 0.292

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 3RVZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
24JS Crystal structure of voltage-gated sodium channel NavAb N49K mutant Deposited 2026-03-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Mutation：N49K 1N7 CHAPSO × 4 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 8 LMT DODECYL-BETA-D-MALTOSIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；9%-11% PEG MME 2000, 100mM sodium chloride, 100mM magnesium nitrate, 25mM cadmium nitrate, 100mM Tris-HCl, pH 8.4
Resolution 3.50 Å R-free 0.274
24JT Crystal structure of voltage-gated sodium channel NavAb N49K mutant Deposited 2026-03-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–229（229 aa）
Mutation：N49K LMT DODECYL-BETA-D-MALTOSIDE × 4 1N7 CHAPSO × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；7%-9% PEG 6000, 100mM sodium chloride, 100mM magnesium nitrate, 100mM cadmium nitrate, 10mM copper chloride, 100mM Tris-HCl, pH 8.4
Resolution 4.10 Å R-free 0.375
24JU Crystal structure of voltage-gated sodium channel NavAb N49K mutant Deposited 2026-03-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–229（229 aa）
Mutation：N49K LMT DODECYL-BETA-D-MALTOSIDE × 4 1N7 CHAPSO × 4 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 32 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；7%-9% PEG 6000, 100mM sodium chloride, 100mM magnesium nitrate, 100mM cadmium nitrate, 10mM copper chloride, 100mM Tris-HCl, pH 8.4
Resolution 3.70 Å R-free 0.320
3RVY Crystal structure of the NavAb voltage-gated sodium channel (Ile217Cys, 2.7 A) Deposited 2011-05-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Chain B 1–267（267 aa）
Mutation：I217C Mutation：I217C PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.75；298 K；CHAPSO:DMPC bicelles, 2 M ammonium sulphate, 0.1 M Na-citrate pH 4.75, 28% glucose, 0.01 M YCl3, nicotinic acid (sat.), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.70 Å R-free 0.273
3RW0 Crystal structure of the NavAb voltage-gated sodium channel (Met221Cys, 2.95 A) Deposited 2011-05-06 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Chain B 1–267（267 aa）
Mutation：M221C Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：M221C Non-standard monomer：Yes (specific site not provided by mmCIF) PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.75；298 K；CHAPSO:DMPC bicelles, 2 M ammonium sulphate, 0.1 M Na-citrate pH 4.75, 28% glucose, nicotinic acid (sat.), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.95 Å R-free 0.272
4EKW Crystal structure of the NavAb voltage-gated sodium channel (wild-type, 3.2 A) Deposited 2012-04-10 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Chain B 1–267（267 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 6 PO4 PHOSPHATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.75；298 K；CHAPSO:DMPC BICELLES, 2 M AMMONIUM SULPHATE, 0.1 M NA-CITRATE, 28% GLUCOSE, NICOTINIC ACID, pH 4.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.21 Å R-free 0.322
4EKW Crystal structure of the NavAb voltage-gated sodium channel (wild-type, 3.2 A) Deposited 2012-04-10 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain C 1–267（267 aa）
Chain D 1–267（267 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 4 PO4 PHOSPHATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.75；298 K；CHAPSO:DMPC BICELLES, 2 M AMMONIUM SULPHATE, 0.1 M NA-CITRATE, 28% GLUCOSE, NICOTINIC ACID, pH 4.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.21 Å R-free 0.322
4MS2 Structural basis of Ca2+ selectivity of a voltage-gated calcium channel Deposited 2013-09-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–219（219 aa）
Chain B 1–219（219 aa）
Chain C 1–219（219 aa）
Chain D 1–219（219 aa）
Not recorded PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.75；298 K；0.1M Na-citrate, pH 4.75, 2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.75 Å R-free 0.255
4MTF Structural Basis of Ca2+ Selectivity of a Voltage-gated Calcium Channel Deposited 2013-09-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–219（219 aa）
Chain B 1–219（219 aa）
Chain C 1–219（219 aa）
Chain D 1–219（219 aa）
Not recorded CA CALCIUM ION × 2 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.75；298 K；0.1M Na-citrate,pH4.75, 2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.272
4MTG Structural Basis for Ca2+ Selectivity of a Voltage-gated Calcium Channel Deposited 2013-09-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–219（219 aa）
Chain B 1–219（219 aa）
Chain C 1–219（219 aa）
Chain D 1–219（219 aa）
Not recorded CA CALCIUM ION × 2 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.75；298 K；0.1M Na-citrate,pH 4.75, 2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.30 Å R-free 0.273
4MTO Structural Basis for Ca2+ Selectivity of a Voltage-gated Calcium Channel Deposited 2013-09-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–219（219 aa）
Chain B 1–219（219 aa）
Chain C 1–219（219 aa）
Chain D 1–219（219 aa）
Not recorded CA CALCIUM ION × 3 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.75；298 K；0.1M Na-citrate,pH 4.75, 2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.40 Å R-free 0.297
4MVM Structural Basis for Ca2+ Selectivity of a Voltage-gated Calcium Channel Deposited 2013-09-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–219（219 aa） Fragment：Voltage-gated Calcium Channel (Residues 1-219)
Chain B 1–219（219 aa） Fragment：Voltage-gated Calcium Channel (Residues 1-219)
Chain C 1–219（219 aa） Fragment：Voltage-gated Calcium Channel (Residues 1-219)
Chain D 1–219（219 aa） Fragment：Voltage-gated Calcium Channel (Residues 1-219)
Not recorded PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 16 CA CALCIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.75；298 K；CHAPSO:DMPC BICELLES,0.1M Na-Acetate ,pH4.75, 2M Ammonium Sulfate, 28% Glucose, 10mM Calcium Chloride., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.275
4MVO Structural Basis for Ca2+ Selectivity of a Voltage-gated Calcium Channel Deposited 2013-09-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–219（219 aa） Fragment：Voltage-gated Calcium Channel (Residues 1-219)
Chain B 1–219（219 aa） Fragment：Voltage-gated Calcium Channel (Residues 1-219)
Chain C 1–219（219 aa） Fragment：Voltage-gated Calcium Channel (Residues 1-219)
Chain D 1–219（219 aa） Fragment：Voltage-gated Calcium Channel (Residues 1-219)
Not recorded PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 16 CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.75；298 K；CHAPSO:DMPC BICELLES, 0.1M Na-Acetate, pH4.75, 2M Ammonium Sulfate, 28% Glucose, 15mM Calcium Chloride., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.30 Å R-free 0.279
4MVQ Structural Basis for Ca2+ Selectivity of a Voltage-gated Calcium Channel Deposited 2013-09-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–219（219 aa）
Chain B 1–219（219 aa）
Chain C 1–219（219 aa）
Chain D 1–219（219 aa）
Not recorded CA CALCIUM ION × 2 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.75；298 K；CHAPSO:DMPC BICELLES,0.1M Na-Acetate ,pH4.75, 2M Ammonium Sulfate, 28% Glucose, 15mM Calcium Chloride., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.40 Å R-free 0.313
4MVR Structural Basis for Ca2+ Selectivity of a Voltage-gated Calcium Channel Deposited 2013-09-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–219（219 aa）
Chain B 1–219（219 aa）
Chain C 1–219（219 aa）
Chain D 1–219（219 aa）
Not recorded MN MANGANESE (II) ION × 1 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；CHAPSO:DMPC BICELLES, 0.1M Na-Acetate, pH5.0, 2M Ammonium Sulfate, 28% Glucose, 10mM Mn2+, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.262
4MVS Structural Basis for Ca2+ Selectivity of a Voltage-gated Calcium Channel Deposited 2013-09-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–219（219 aa）
Chain B 1–219（219 aa）
Chain C 1–219（219 aa）
Chain D 1–219（219 aa）
Not recorded CD CADMIUM ION × 5 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.75；298 K；CHAPSO:DMPC bicelles, 0.1M Na-Acetate, pH4.75, 2M Ammonium Sulfate, 28% Glucose, 100mM Mn2+, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.30 Å R-free 0.269
4MVU Structural Basis for Ca2+ Selectivity of a Voltage-gated Calcium Channel Deposited 2013-09-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–219（219 aa）
Chain B 1–219（219 aa）
Chain C 1–219（219 aa）
Chain D 1–219（219 aa）
Not recorded PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 16 CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.75；298 K；CHAPSO:DMPC bicelles, 0.1M Na-Acetate, pH4.75, 2M Ammonium Sulfate, 28% Glucose, 15mM Calcium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.20 Å R-free 0.263
4MVZ Structural Basis for Ca2+ Selectivity of a Voltage-gated Calcium Channel Deposited 2013-09-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–219（219 aa）
Chain B 1–219（219 aa）
Chain C 1–219（219 aa）
Chain D 1–219（219 aa）
Not recorded CA CALCIUM ION × 2 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.75；298 K；CHAPSO:DMPC bicelles, 0.1M Na-Acetate, pH 4.75, 2M Ammonium Sulfate, 28% Glucose, 15mM Calcium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.30 Å R-free 0.280
4MW3 Structural Basis for Ca2+ Selectivity of a Voltage-gated Calcium Channel Deposited 2013-09-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–219（219 aa）
Chain B 1–219（219 aa）
Chain C 1–219（219 aa）
Chain D 1–219（219 aa）
Not recorded CA CALCIUM ION × 3 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.75；298 K；CHAPSO:DMPC bicelles, 0.1M Na-Acetate,pH 4.75, 2M Ammonium Sulfate, 28% Glucose, 15mM Calcium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.30 Å R-free 0.267
4MW8 Structural Basis for Ca2+ Selectivity of a Voltage-gated Calcium Channel Deposited 2013-09-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–219（219 aa）
Chain B 1–219（219 aa）
Chain C 1–219（219 aa）
Chain D 1–219（219 aa）
Not recorded CA CALCIUM ION × 2 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.75；298 K；CHAPSO:DMPC bicelles, 0.1M Na-Acetate,pH 4.75, 2M Ammonium Sulfate, 28% Glucose, 15mM Calcium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.26 Å R-free 0.314
5EK0 Human Nav1.7-VSD4-NavAb in complex with GX-936. Deposited 2015-11-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–23（23 aa）
Chain A 58–78（21 aa）
Chain A 109–267（159 aa）
Chain B 1–23（23 aa）
Chain B 58–78（21 aa）
Chain B 109–267（159 aa）
Chain C 1–23（23 aa）
Chain C 58–78（21 aa）
Chain C 109–267（159 aa）
Chain D 1–23（23 aa）
Chain D 58–78（21 aa）
Chain D 109–267（159 aa）
Not recorded PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 21 5P2 3-cyano-4-[2-[2-(1-ethylazetidin-3-yl)pyrazol-3-yl]-4-(trifluoromethyl)phenoxy]-~{N}-(1,2,4-thiadiazol-5-yl)benzenesulfonamide × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.4；277 K；2.2 ammonium sulfate, 100 mM sodium citrate pH 5.4
Resolution 3.53 Å R-free 0.272
5KLB Crystal structure of the CavAb voltage-gated calcium channel(wild-type, 2.7A) Deposited 2016-06-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Chain B 1–267（267 aa）
Chain C 1–267（267 aa）
Chain D 1–267（267 aa）
Not recorded MC3 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 20 CA CALCIUM ION × 3 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；CHAPSO:DMPC BICELLES,0.1M Na-citrate,pH5.0,2M Ammonium Sulfate
Resolution 2.70 Å R-free 0.260
5KLG Structure of CavAb(W195Y) in complex with Br-dihydropyridine derivative UK-59811 Deposited 2016-06-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Chain B 1–267（267 aa）
Chain C 1–267（267 aa）
Chain D 1–267（267 aa）
Not recorded CA CALCIUM ION × 2 MC3 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 11 6UC O3-ethyl O5-methyl (4R)-4-(2-bromophenyl)-2-[2-(dimethylamino)ethoxymethyl]-6-methyl-1,4-dihydropyridine-3,5-dicarboxylate × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；CHAPSO:DMPC BICELLES,0.1M Na-citrate,pH5.0,2M Ammonium Sulfate
Resolution 3.30 Å R-free 0.303
5KLS Structure of CavAb in complex with Br-dihydropyridine derivative UK-59811 Deposited 2016-06-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Chain B 1–267（267 aa）
Chain C 1–267（267 aa）
Chain D 1–267（267 aa）
Not recorded MC3 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 15 CA CALCIUM ION × 2 6UC O3-ethyl O5-methyl (4R)-4-(2-bromophenyl)-2-[2-(dimethylamino)ethoxymethyl]-6-methyl-1,4-dihydropyridine-3,5-dicarboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；CHAPSO:DMPC BICELLES,0.1M Na-citrate,pH5.0,2M Ammonium Sulfate 100uM UK-59811
Resolution 3.30 Å R-free 0.300
5KMD Structure of CavAb in complex with amlodipine Deposited 2016-06-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Chain B 1–267（267 aa）
Chain C 1–267（267 aa）
Chain D 1–267（267 aa）
Not recorded MC3 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 14 CA CALCIUM ION × 2 6UB amlodipine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；CHAPSO:DMPC BICELLES,0.1M Na-citrate,pH5.0,2M Ammonium Sulfate ,100uM amlodipine
Resolution 3.20 Å R-free 0.277
5KMF Structure of CavAb in complex with nimodipine Deposited 2016-06-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Chain B 1–267（267 aa）
Chain C 1–267（267 aa）
Chain D 1–267（267 aa）
Not recorded 6U9 S-nimodipine × 1 MC3 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 14 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；CHAPSO:DMPC BICELLES,0.1M Na-citrate,pH5.0,2M Ammonium Sulfate,100uM nimodipine
Resolution 3.20 Å R-free 0.256
5KMH Structure of CavAb in complex with Br-verapamil Deposited 2016-06-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Chain B 1–267（267 aa）
Chain C 1–267（267 aa）
Chain D 1–267（267 aa）
Not recorded CA CALCIUM ION × 3 MC3 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 6 PX6 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE × 4 6U8 (2~{R})-2-(2-bromophenyl)-5-[2-(3,4-dimethoxyphenyl)ethyl-methyl-amino]-2-propan-2-yl-pentanenitrile × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；CHAPSO:DMPC BICELLES,0.1M Na-citrate,pH5.0,2M Ammonium Sulfate,100uM Br-verapamil
Resolution 3.20 Å R-free 0.294
5VB2 Crystal structure of the NavAb voltage-gated sodium channel in a closed conformation Deposited 2017-03-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Chain B 1–267（267 aa）
Chain C 1–267（267 aa）
Chain D 1–267（267 aa）
Mutation：T206F, V213Y Mutation：T206F, V213Y Mutation：T206F, V213Y Mutation：T206F, V213Y CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 8 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 13 PO4 PHOSPHATE ION × 4 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；1.8 M ammonium sulfate and 100 mM sodium acetate, 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC):CHAPSO bicelles
Resolution 3.20 Å R-free 0.266
5VB8 Crystal structure of the NavAb voltage-gated sodium channel in an open state Deposited 2017-03-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–226（226 aa） Fragment：UNP residues 1-226
Not recorded NA SODIUM ION × 4 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 16 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；277.15 K；1.8 M ammonium sulfate and 100 mM sodium acetate (pH 4.8). 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC):CHAPSO bicelles (Anatrace)
Resolution 2.85 Å R-free 0.254
6C1E NavAb NormoPP mutant Deposited 2018-01-04 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Chain B 1–267（267 aa）
Mutation：C235I, H123R Mutation：C235I, H123R PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 36 BNC 5-BETA-24-NOR-CHOLANE-3(ALPHA),7(ALPHA),12(ALPHA)-TRIOL × 2 UHH (3ALPHA,5ALPHA,7ALPHA,8ALPHA,12ALPHA,14BETA,17ALPHA)-3,7,12-TRIHYDROXYCHOL-1-EN-24-AMIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；277 K；ammonium sulphate, Na-citrate
Resolution 2.86 Å R-free 0.240
6C1K HypoPP mutant with ligand1 Deposited 2018-01-04 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Chain B 1–267（267 aa）
Mutation：C235I, H123R Mutation：C235I, H123R GAI GUANIDINE × 4 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 34 NA SODIUM ION × 8 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；277 K；ammonium sulphate, Na-citrate
Resolution 2.70 Å R-free 0.246
6C1M NavAb NormoPP mutant Deposited 2018-01-04 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Chain B 1–267（267 aa）
Mutation：C235I, H123R Mutation：C235I, H123R PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 30 1N7 CHAPSO × 16 MGX 1-METHYLGUANIDINE × 4 NA SODIUM ION × 8 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 4.8；277 K；ammonium sulphate, Na-citrate
Resolution 2.52 Å R-free 0.227
6C1P HypoPP mutant Deposited 2018-01-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Chain B 1–267（267 aa）
Chain C 1–267（267 aa）
Chain D 1–267（267 aa）
Mutation：C235I, H123R Mutation：C235I, H123R Mutation：C235I, H123R Mutation：C235I, H123R PO4 PHOSPHATE ION × 2 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 15 1N7 CHAPSO × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；277 K；ammonium sulphate, Na-citrate
Resolution 2.90 Å R-free 0.260
6JUH structure of CavAb in complex with efonidipine Deposited 2019-04-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Chain B 1–267（267 aa）
Chain C 1–267（267 aa）
Chain D 1–267（267 aa）
Mutation：E1177D, S1178D, M1181N Mutation：E1177D, S1178D, M1181N Mutation：E1177D, S1178D, M1181N Mutation：E1177D, S1178D, M1181N MC3 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE × 4 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 4 G3P SN-GLYCEROL-3-PHOSPHATE × 4 CA CALCIUM ION × 2 C9X 2-[phenyl-(phenylmethyl)amino]ethyl (4~{R})-5-(5,5-dimethyl-2-oxidanylidene-1,3,2$l^{5}-dioxaphosphinan-2-yl)-2,6-dimethyl-4-(3-nitrophenyl)-1,4-dihydropyridine-3-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；1.0-2.0M Ammonium Sulfate 100 mM Na-citrate pH=5.0
Resolution 3.00 Å R-free 0.291
6KE5 Structure of CavAb in complex with Diltiazem and Amlodipine Deposited 2019-07-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Chain B 1–267（267 aa）
Chain C 1–267（267 aa）
Chain D 1–267（267 aa）
Not recorded LPC [1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE × 3 CA CALCIUM ION × 3 G3P SN-GLYCEROL-3-PHOSPHATE × 5 6UB amlodipine × 1 D6C [(2~{S},3~{R})-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxidanylidene-2,3-dihydro-1,5-benzothiazepin-3-yl] ethanoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；0.1M Na-citrate,pH5.0,2M Ammonium Sulfate
Resolution 2.80 Å R-free 0.292
6KEB Structure basis for Diltiazem block of a voltage-gated calcium channel Deposited 2019-07-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Chain B 1–267（267 aa）
Chain C 1–267（267 aa）
Chain D 1–267（267 aa）
Not recorded PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 12 CA CALCIUM ION × 2 D6C [(2~{S},3~{R})-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxidanylidene-2,3-dihydro-1,5-benzothiazepin-3-yl] ethanoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；CHAPSO:DMPC BICELLES,0.1M Na-citrate,pH5.0,2M Ammonium Sulfate
Resolution 3.20 Å R-free 0.277
6MVV NavAb voltage-gated sodium channel, I217C/F203A Deposited 2018-10-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Chain B 1–267（267 aa）
Chain C 1–267（267 aa）
Chain D 1–267（267 aa）
Mutation：F203A, I217C Mutation：F203A, I217C Mutation：F203A, I217C Mutation：F203A, I217C PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 6 PO4 PHOSPHATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；1.8 M Ammonium Sulfate 100mM Sodium Acetate, pH 5.0
Resolution 2.90 Å R-free 0.256
6MVW NavAb voltage-gated sodium channel, I217C/F203W Deposited 2018-10-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Chain B 1–267（267 aa）
Chain C 1–267（267 aa）
Chain D 1–267（267 aa）
Mutation：I217C, F203W Mutation：I217C, F203W Mutation：I217C, F203W Mutation：I217C, F203W PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 10 PO4 PHOSPHATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；1.8 M Ammonium Sulfate, 100 mM Sodium Acetate
Resolution 3.20 Å R-free 0.246
6MVX NavAb Voltage-gated Sodium Channel, I217C, in Complex with Class 1C Anti-arrhythmic Flecainide Deposited 2018-10-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Chain B 1–267（267 aa）
Chain C 1–267（267 aa）
Chain D 1–267（267 aa）
Mutation：I217C Mutation：I217C Mutation：I217C Mutation：I217C PO4 PHOSPHATE ION × 10 K4D Flecainide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；1.8 M Ammonium Sulfate 100 mM Sodium Acetate, pH 5.0 100 uM Flecainide
Resolution 3.46 Å R-free 0.263
6MVY NavAb voltage-gated sodium channel, residues 1-226, crystallized in the presence of Class 1B Anti-arrhythmic drug Lidocaine Deposited 2018-10-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–226（226 aa）
Mutation：I217C PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 16 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；1.8 M Ammonium Sulfate 100 mM Sodium Acetate, pH 5.0 10 mM Lidocaine
Resolution 3.00 Å R-free 0.237
6MVY NavAb voltage-gated sodium channel, residues 1-226, crystallized in the presence of Class 1B Anti-arrhythmic drug Lidocaine Deposited 2018-10-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain B 1–226（226 aa）
Mutation：I217C PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 16 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；1.8 M Ammonium Sulfate 100 mM Sodium Acetate, pH 5.0 10 mM Lidocaine
Resolution 3.00 Å R-free 0.237
6MWA NavAb Voltage-gated Sodium Channel, residues 1-239 Deposited 2018-10-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain B 1–239（239 aa）
Not recorded PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 16 SO4 SULFATE ION × 4 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；1.8 M Ammonium Sulfate 100mM Sodium Acetate pH 5.8
Resolution 2.40 Å R-free 0.249
6MWB NavAb Voltage-gated Sodium Channel, residues 1-239 with mutation T206A Deposited 2018-10-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain B 1–239（239 aa）
Mutation：T206A PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 16 SO4 SULFATE ION × 4 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；1.8 M Ammonium Sulfate 100 mM Sodium Acetate pH 5.8
Resolution 2.60 Å R-free 0.236
6MWD NavAb Voltage-gated Sodium Channel, residues 1-239 with mutation T206S Deposited 2018-10-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain B 1–239（239 aa）
Mutation：T206S PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 16 ACT ACETATE ION × 4 SO4 SULFATE ION × 4 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；1.8 Ammonium Sulfate 100 mM Sodium Acetate, pH 5.8
Resolution 2.33 Å R-free 0.250
6MWG NavAb Voltage-gated Sodium Channel, residues 1-239, with mutation T206V Deposited 2018-10-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain B 1–239（239 aa）
Mutation：T206V PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 16 ACT ACETATE ION × 4 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；1.8 M Ammonium Sulfate 100 mM Sodium Acetate, pH 5.8
Resolution 2.50 Å R-free 0.239
6N4Q CryoEM structure of Nav1.7 VSD2 (actived state) in complex with the gating modifier toxin ProTx2 Deposited 2018-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–25（25 aa）
Chain A 58–78（21 aa）
Chain A 107–267（161 aa）
Chain B 1–25（25 aa）
Chain B 58–78（21 aa）
Chain B 107–267（161 aa）
Chain C 1–25（25 aa）
Chain C 58–78（21 aa）
Chain C 107–267（161 aa）
Chain D 1–25（25 aa）
Chain D 58–78（21 aa）
Chain D 107–267（161 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；10 mM Tris pH 8.0, 100 mM NaCl, 0.06% FA3, 0.1 mg/ml POPC:POPE:POPG mixed at molar ratio 3:1:1
cryo-EM vitrification conditions Cryogen ETHANE；Apply 3 uL, blot 2.5s. Ted Pella 595 filter paper.
Resolution 3.60 Å
6N4R CryoEM structure of Nav1.7 VSD2 (deactived state) in complex with the gating modifier toxin ProTx2 Deposited 2018-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–25（25 aa）
Chain A 58–78（21 aa）
Chain A 107–267（161 aa）
Chain B 1–25（25 aa）
Chain B 58–78（21 aa）
Chain B 107–267（161 aa）
Chain C 1–25（25 aa）
Chain C 58–78（21 aa）
Chain C 107–267（161 aa）
Chain D 1–25（25 aa）
Chain D 58–78（21 aa）
Chain D 107–267（161 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；10 mM Tris pH 8.0, 100 mM NaCl, 0.06% FA3, 0.1 mg/ml POPC:POPE:POPG mixed at molar ratio 3:1:1
cryo-EM vitrification conditions Cryogen ETHANE；Apply 3 uL, blot 2.5s. Ted Pella 595 filter paper.
Resolution 4.20 Å
6P6W Cryo-EM structure of voltage-gated sodium channel NavAb N49K/L109A/M116V/G94C/Q150C disulfide crosslinked mutant in the resting state Deposited 2019-06-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Chain B 1–267（267 aa）
Chain C 1–267（267 aa）
Chain D 1–267（267 aa）
Mutation：R4A, N49K, L109A, M116V, G94C, Q150C,R4A, N49K, L109A, M116V, G94C, Q150C Mutation：R4A, N49K, L109A, M116V, G94C, Q150C,R4A, N49K, L109A, M116V, G94C, Q150C Mutation：R4A, N49K, L109A, M116V, G94C, Q150C,R4A, N49K, L109A, M116V, G94C, Q150C Mutation：R4A, N49K, L109A, M116V, G94C, Q150C,R4A, N49K, L109A, M116V, G94C, Q150C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6P6X Crystal structure of voltage-gated sodium channel NavAb G94C/Q150C mutant in the activated state Deposited 2019-06-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–239（239 aa）
Mutation：G94C, Q150C PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 36 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；1.8 M ammonium sulfate 0.1 M sodium citrate pH 5.6
Resolution 2.75 Å R-free 0.265
6P6Y Crystal structure of voltage-gated sodium channel NavAb V100C/Q150C disulfide crosslinked mutant in the activated state Deposited 2019-06-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–239（239 aa）
Mutation：V100C, Q150C CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 8 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；277 K；1.8 M ammonium sulfate 0.1 M sodium citrate pH 4.8
Resolution 2.89 Å R-free 0.273
7K48 Structure of NavAb/Nav1.7-VS2A chimera trapped in the resting state by tarantula toxin m3-Huwentoxin-IV Deposited 2020-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–17（17 aa）
Chain A 60–83（24 aa）
Chain A 106–239（134 aa）
Chain B 1–17（17 aa）
Chain B 60–83（24 aa）
Chain B 106–239（134 aa）
Chain C 1–17（17 aa）
Chain C 60–83（24 aa）
Chain C 106–239（134 aa）
Chain D 1–17（17 aa）
Chain D 60–83（24 aa）
Chain D 106–239（134 aa）
Mutation：R398A,L506A,M513V Mutation：R398A,L506A,M513V Mutation：R398A,L506A,M513V Mutation：R398A,L506A,M513V Mutation：R398A,L506A,M513V Mutation：R398A,L506A,M513V Mutation：R398A,L506A,M513V Mutation：R398A,L506A,M513V Mutation：R398A,L506A,M513V Mutation：R398A,L506A,M513V Mutation：R398A,L506A,M513V Mutation：R398A,L506A,M513V No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 2.5-4.0 seconds before plunging
Resolution 3.60 Å
8DIV Crystal structure of NavAb I22V as a basis for the human Nav1.7 Inherited Erythromelalgia I136V mutation Deposited 2022-06-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–239（239 aa）
Mutation：I22V BGC beta-D-glucopyranose × 4 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；1.7-1.8 M Ammonium sulfate 0.1 M Sodium Citrate pH 5.0
Resolution 2.54 Å R-free 0.237
8DIW Crystal structure of NavAb E96P as a basis for the human Nav1.7 Inherited Erythromelalgia S211P mutation Deposited 2022-06-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–239（239 aa）
Mutation：E96P PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；1.7-1.8 M Ammonium Sulfate 0.1 M Sodium Citrate pH 5.4
Resolution 3.11 Å R-free 0.272
8DIX Structure of NavAb L98R as a basis for the human Nav1.7 Inherited Erythromelalgia L823R mutation Deposited 2022-06-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–239（239 aa）
Mutation：L98R PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；277 K；1.8-1.9 M Ammonium Sulfate 0.1 M Sodium Citrate pH 4.8
Resolution 3.30 Å R-free 0.255
8DIY Crystal structure of NavAb L101S as a basis for the human Nav1.7 Inherited Erythromelalgia F216S mutation Deposited 2022-06-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–239（239 aa）
Mutation：L101S PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；277 K；1.7-1.8 M Ammonium Sulfate 0.1 M Sodium Citrate pH 4.8
Resolution 2.85 Å R-free 0.254
8DIZ Crystal structure of NavAb I119T as a basis for the human Nav1.7 Inherited Erythromelalgia I234T mutation Deposited 2022-06-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–239（239 aa）
Mutation：I119T PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；1.8-1.9 M Ammonium Sulfate 0.1 M Sodium Citrate pH 4.6
Resolution 2.75 Å R-free 0.255
8DJ0 Crystal structure of NavAb L123T as a basis for the human Nav1.7 Inherited Erythromelalgia I848T mutation Deposited 2022-06-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–239（239 aa）
Mutation：L123T PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；1.9 M Ammonium sulfate 0.1 M Sodium Citrate pH 4.6
Resolution 2.70 Å R-free 0.248
8DJ1 Crystal structure of NavAb V126T as a basis for the human Nav1.7 Inherited Erythromelalgia S241T mutation Deposited 2022-06-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–239（239 aa）
Mutation：V126T PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；277 K；1.8 M Ammonium Sulfate 0.1 M Sodium Citrate pH 5.2
Resolution 3.10 Å R-free 0.260
8H9O Crystal structure of voltage-gated sodium channel NavAb N49K mutant in sodium ion condition Deposited 2022-10-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Mutation：N49K LMT DODECYL-BETA-D-MALTOSIDE × 8 1N7 CHAPSO × 4 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 36 NA SODIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；9%-11% PEG MME 2000, 100 mM sodium chloride, 100 mM magnesium nitrate, 25 mM cadmium nitrate, 100 mM Tris-HCl, pH 8.4
Resolution 3.30 Å R-free 0.272
8H9W Crystal structure of voltage-gated sodium channel NavAb N49K mutant in calcium ion condition Deposited 2022-10-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Mutation：N49K LMT DODECYL-BETA-D-MALTOSIDE × 8 1N7 CHAPSO × 4 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 32 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；9%-11% PEG MME 2000, 100 mM sodium chloride, 100 mM magnesium nitrate, 25 mM cadmium nitrate, 100 mM Tris-HCl, pH 8.4
Resolution 2.70 Å R-free 0.264
8H9X Crystal structure of voltage-gated sodium channel NavAb N49K/L176Q mutant in sodium ion condition Deposited 2022-10-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Mutation：N49K, L176Q LMT DODECYL-BETA-D-MALTOSIDE × 8 1N7 CHAPSO × 4 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 32 NA SODIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；9%-11% PEG MME 2000, 100 mM sodium chloride, 100 mM magnesium nitrate, 25 mM cadmium nitrate, 100 mM Tris-HCl, pH 8.4
Resolution 3.40 Å R-free 0.280
8H9Y Crystal structure of voltage-gated sodium channel NavAb N49K/L176Q mutant in calcium ion condition Deposited 2022-10-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Mutation：N49K, L176Q LMT DODECYL-BETA-D-MALTOSIDE × 8 1N7 CHAPSO × 4 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 32 CA CALCIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；9%-11% PEG MME 2000, 100 mM sodium chloride, 100 mM magnesium nitrate, 25 mM cadmium nitrate, 100 mM Tris-HCl, pH 8.4
Resolution 3.40 Å R-free 0.264
8HA1 Crystal structure of voltage-gated sodium channel NavAb N49K/L176G mutant in sodium ion condition Deposited 2022-10-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Mutation：N49K, L176G LMT DODECYL-BETA-D-MALTOSIDE × 8 1N7 CHAPSO × 4 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 32 NA SODIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；9%-11% PEG MME 2000, 100 mM sodium chloride, 100 mM magnesium nitrate, 25 mM cadmium nitrate, 100 mM Tris-HCl, pH 8.4
Resolution 3.50 Å R-free 0.297
8HA2 Crystal structure of voltage-gated sodium channel NavAb N49K/L176G mutant in calcium ion condition Deposited 2022-10-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Mutation：N49K, L176G LMT DODECYL-BETA-D-MALTOSIDE × 8 1N7 CHAPSO × 4 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 32 CA CALCIUM ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；9%-11% PEG MME 2000, 100 mM sodium chloride, 100 mM magnesium nitrate, 25mM cadmium nitrate, 100 mM Tris-HCl, pH 8.4
Resolution 3.30 Å R-free 0.281
9UC1 Crystal structure of voltage-gated sodium channel NavAb N49K/S178T mutant Deposited 2025-04-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Mutation：N49K, S178T CA CALCIUM ION × 12 1N7 CHAPSO × 4 LMT DODECYL-BETA-D-MALTOSIDE × 4 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 32 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293 K；9%-11% PEG MME 2000, 100mM sodium chloride, 100mM magnesium nitrate, 25mM cadmium nitrate, 100mM Tris-HCl, pH 8.4
Resolution 2.50 Å R-free 0.274
9UC2 Crystal structure of voltage-gated sodium channel NavAb N49K/S178A mutant Deposited 2025-04-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Mutation：N49K,S178A CA CALCIUM ION × 12 1N7 CHAPSO × 4 LMT DODECYL-BETA-D-MALTOSIDE × 4 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 32 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293 K；9%-11% PEG MME 2000, 100mM sodium chloride, 100mM magnesium nitrate, 25mM cadmium nitrate, 100mM Tris-HCl, pH 8.4
Resolution 2.80 Å R-free 0.294
9UC3 Crystal structure of voltage-gated sodium channel NavAb N49K/S178G mutant Deposited 2025-04-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Mutation：N49K,S178G CA CALCIUM ION × 12 1N7 CHAPSO × 4 LMT DODECYL-BETA-D-MALTOSIDE × 4 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 32 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；293 K；9%-11% PEG MME 2000, 100mM sodium chloride, 100mM magnesium nitrate, 25mM cadmium nitrate, 100mM Tris-HCl, pH 8.4
Resolution 2.90 Å R-free 0.299
9UC4 Crystal structure of voltage-gated sodium channel NavAb N49K/S178T/T206A mutant Deposited 2025-04-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Mutation：N49K, S178T, T206A CA CALCIUM ION × 12 1N7 CHAPSO × 4 LMT DODECYL-BETA-D-MALTOSIDE × 4 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 32 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；9%-11% PEG MME 2000, 100mM sodium chloride, 100mM magnesium nitrate, 25mM cadmium nitrate, 100mM Tris-HCl, pH 8.4
Resolution 3.40 Å R-free 0.312
9VDQ Crystal structure of voltage-gated sodium channel NavAb N49K mutant Deposited 2025-06-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Mutation：N49K NA SODIUM ION × 12 1N7 CHAPSO × 4 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 32 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；9%-11% PEG MME 2000, 100mM sodium chloride, 100mM magnesium nitrate, 25mM cadmium nitrate, 100mM Tris-HCl, pH 8.4
Resolution 3.10 Å R-free 0.289
9VDR Crystal structure of voltage-gated sodium channel NavAb N49K/L176F mutant Deposited 2025-06-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Mutation：N49K/L176F NA SODIUM ION × 8 1N7 CHAPSO × 4 LMT DODECYL-BETA-D-MALTOSIDE × 4 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；9%-11% PEG MME 2000, 100 mM sodium chloride, 100mM magnesium nitrate, 25mM cadmium nitrate, 100mM Tris-HCl, pH 8.4
Resolution 3.70 Å R-free 0.327
9VDS Crystal structure of voltage-gated sodium channel NavAb N49K/L176W mutant Deposited 2025-06-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Mutation：N49K/L176W NA SODIUM ION × 4 1N7 CHAPSO × 4 LMT DODECYL-BETA-D-MALTOSIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；9%-11% PEG MME 2000, 100mM sodium chloride, 100mM magnesium nitrate, 25mM cadmium nitrate, 100mM Tris-HCl, pH 8.4
Resolution 3.70 Å R-free 0.339
9VDT Crystal structure of voltage-gated sodium channel NavAb N49K DC230 mutant Deposited 2025-06-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–267（267 aa）
Mutation：N49K NA SODIUM ION × 8 1N7 CHAPSO × 4 LMT DODECYL-BETA-D-MALTOSIDE × 4 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 32 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；7%-9% PEG 6000, 100mM sodium chloride, 100mM magnesium nitrate, 100mM cadmium chloride, 10mM copper chloride, 100mM Tris-HCl, pH 8.4
Resolution 3.50 Å R-free 0.344
9VDU Crystal structure of voltage-gated sodium channel NavAb N49K/L176F DC230 mutant Deposited 2025-06-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–230（230 aa）
Mutation：N49K/L176F NA SODIUM ION × 8 1N7 CHAPSO × 4 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 28 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；7%-9% PEG 6000, 100mM sodium chloride, 100mM magnesium nitrate, 100mM cadmium chloride, 10mM copper chloride, 100mM Tris-HCl, pH 8.4
Resolution 3.40 Å R-free 0.304

71 other PDB entries and 73 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A8EVM5_ARCB4
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 19–285； UniProt 1–267 Author chain B； PDBConstruct 19–285； UniProt 1–267

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

SAXS scattering curve SAXS Profile

SAXS profile for 3rvz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3rvz
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id3rvz
Deposition date deposition_date2011-05-06
Structure title titleCrystal structure of the NavAb voltage-gated sodium channel (Ile217Cys, 2.8 A)
Keywords keywordstetrameric ion channel, voltage-gated sodium-selective ion channel, membrane, METAL TRANSPORT; METAL TRANSPORT
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier29.98 Å
Radius of gyration Rg (electron density) rg_electron29.27 Å
Forward intensity I(0) i035479700.00
Molecular weight molecular_weight52944.0 kDa
Excluded volume excluded_volume69136 ų
Envelope volume envelope_volume92215 ų
Hydration-shell volume shell_volume27709 ų
Envelope diameter envelope_diameter96.8 Å
Shell Rg shell_rg34.54 Å
Envelope Rg envelope_rg28.75 Å
Shape Rg shape_rg29.28 Å
Total Rg total_rg29.86 Å
Total atoms total_atoms3726
Residues n_residues438
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax93.0 Å
Rg (real space) rg_real29.92 Å
Rg uncertainty (real space) rg_real_error0.77 Å
I(0) (real space) i0_real3.5480e+07
I(0) uncertainty (real space) i0_real_error5.9140e+05
Rg (reciprocal space) rg_reciprocal29.95 Å
I(0) (reciprocal space) i0_reciprocal35480000.0000
Solution quality estimate total_estimate0.9132
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary40.4 Å
Skewness Skewness skewness0.123
Kurtosis Kurtosis kurtosis-0.659
Angular range angular_range— – 0.2650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2655000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.975; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.958
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3rvza_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.14 — Gated ion channels
Superfamily Superfamily superfamilyf.14.1 — Voltage-gated ion channels
Family Family familyf.14.1.2 — Voltage-gated Na/Ca cation channels
Domain ID domain_idd3rvzb_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.14 — Gated ion channels
Superfamily Superfamily superfamilyf.14.1 — Voltage-gated ion channels
Family Family familyf.14.1.2 — Voltage-gated Na/Ca cation channels

CATH v4.4 (4 domains)

Domain ID domain_id3rvzA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily350 — Voltage-gated potassium channels. Chain C
Domain ID domain_id3rvzA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70 —
Domain ID domain_id3rvzB01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily350 — Voltage-gated potassium channels. Chain C
Domain ID domain_id3rvzB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70 —
▶

8. Citations (1)

▶

9. Files and Curves (10)