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6n4q

CryoEM structure of Nav1.7 VSD2 (actived state) in complex with the gating modifier toxin ProTx2

Method: ELECTRON MICROSCOPY Dmax: 179.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nav1.7 VSD2-NavAb chimera

Arcobacter butzleri (strain RM4018)

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 Insufficient information Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count Chain A； UniProt 1–25 Chain A； UniProt 58–78 Chain A； UniProt 107–267 Chain B； UniProt 1–25 Chain B； UniProt 58–78 Chain B； UniProt 107–267 Chain C； UniProt 1–25 Chain C； UniProt 58–78 Chain C； UniProt 107–267 Chain D； UniProt 1–25 Chain D； UniProt 58–78 Chain D； UniProt 107–267 Not recorded Beta/omega-theraphotoxin-Tp2a × 4 （P83476） Fab light chain × 2 Fab heavy chain × 2 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

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 6N4Q 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 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
3RVZ Crystal structure of the NavAb voltage-gated sodium channel (Ile217Cys, 2.8 A) Deposited 2011-05-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 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 × 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
3RW0 Crystal structure of the NavAb voltage-gated sodium channel (Met221Cys, 2.95 A) Deposited 2011-05-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 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 1–23（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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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
6N4R CryoEM structure of Nav1.7 VSD2 (deactived state) in complex with the gating modifier toxin ProTx2 Deposited 2018-11-20 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 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 experimental conditions 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 19–43； UniProt 1–25 Author chain A； PDBConstruct 75–95； UniProt 58–78 Author chain A； PDBConstruct 128–288； UniProt 107–267 Author chain B； PDBConstruct 19–43； UniProt 1–25 Author chain B； PDBConstruct 75–95； UniProt 58–78 Author chain B； PDBConstruct 128–288； UniProt 107–267 Author chain C； PDBConstruct 19–43； UniProt 1–25 Author chain C； PDBConstruct 75–95； UniProt 58–78 Author chain C； PDBConstruct 128–288； UniProt 107–267 Author chain D； PDBConstruct 19–43； UniProt 1–25 Author chain D； PDBConstruct 75–95； UniProt 58–78 Author chain D； PDBConstruct 128–288； UniProt 107–267

Nav1.7 VSD2-NavAb chimera

Arcobacter butzleri (strain RM4018)

UniProt Q15858

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count Chain A； UniProt 747–777 Chain A； UniProt 811–842 Chain B； UniProt 747–777 Chain B； UniProt 811–842 Chain C； UniProt 747–777 Chain C； UniProt 811–842 Chain D； UniProt 747–777 Chain D； UniProt 811–842 Not recorded Beta/omega-theraphotoxin-Tp2a × 4 （P83476） Fab light chain × 2 Fab heavy chain × 2 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

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 6N4Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
21TP Open-state structure of veratridine-activated human Nav1.7 Deposited 2025-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 Y01 CHOLESTEROL HEMISUCCINATE × 4 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 8 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 A1E26 Veratridine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
21TQ The structure of Nav1.7 with veratridine standing near the IFM motif (site I) Deposited 2025-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 8 A1E26 Veratridine × 1 Y01 CHOLESTEROL HEMISUCCINATE × 4 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 P3X (5E,17R,20S)-23-amino-20-hydroxy-14,20-dioxo-15,19,21-trioxa-20lambda~5~-phosphatricos-5-en-17-yl hexadecanoate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
5EK0 Human Nav1.7-VSD4-NavAb in complex with GX-936. Deposited 2015-11-03 Different construct 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 1527–1559（33 aa）
Chain A 1581–1622（42 aa）
Chain B 1527–1559（33 aa）
Chain B 1581–1622（42 aa）
Chain C 1527–1559（33 aa）
Chain C 1581–1622（42 aa）
Chain D 1527–1559（33 aa）
Chain D 1581–1622（42 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
6J8G Structure of human voltage-gated sodium channel Nav1.7 in complex with auxiliary beta subunits, huwentoxin-IV and saxitoxin (Y1755 up) Deposited 2019-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 9SL [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6J8H Structure of human voltage-gated sodium channel Nav1.7 in complex with auxiliary beta subunits, huwentoxin-IV and saxitoxin (Y1755 down) Deposited 2019-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 9SL [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6J8I Structure of human voltage-gated sodium channel Nav1.7 in complex with auxiliary beta subunits, ProTx-II and tetrodotoxin (Y1755 up) Deposited 2019-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 9SR (1R,5R,6R,7R,9S,11S,12S,13S,14S)-3-amino-14-(hydroxymethyl)-8,10-dioxa-2,4-diazatetracyclo[7.3.1.1~7,11~.0~1,6~]tetradec-3-ene-5,9,12,13,14-pentol (non-preferred name) × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6J8J Structure of human voltage-gated sodium channel Nav1.7 in complex with auxiliary beta subunits, ProTx-II and tetrodotoxin (Y1755 down) Deposited 2019-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 9SR (1R,5R,6R,7R,9S,11S,12S,13S,14S)-3-amino-14-(hydroxymethyl)-8,10-dioxa-2,4-diazatetracyclo[7.3.1.1~7,11~.0~1,6~]tetradec-3-ene-5,9,12,13,14-pentol (non-preferred name) × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6N4R CryoEM structure of Nav1.7 VSD2 (deactived state) in complex with the gating modifier toxin ProTx2 Deposited 2018-11-20 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 747–777（31 aa）
Chain A 811–842（32 aa）
Chain B 747–777（31 aa）
Chain B 811–842（32 aa）
Chain C 747–777（31 aa）
Chain C 811–842（32 aa）
Chain D 747–777（31 aa）
Chain D 811–842（32 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
6NT3 Cryo-EM structure of a human-cockroach hybrid Nav channel. Deposited 2019-01-28 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 1500–1631（132 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 Y01 CHOLESTEROL HEMISUCCINATE × 1 76F (7E,21R,24S)-27-amino-24-hydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaheptacos-7-en-21-yl (9Z,12E)-octadeca-9,12-dienoate × 4 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 1 AJP Digitonin × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6NT4 Cryo-EM structure of a human-cockroach hybrid Nav channel bound to alpha-scorpion toxin AaH2. Deposited 2019-01-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1500–1631（132 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 76F (7E,21R,24S)-27-amino-24-hydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaheptacos-7-en-21-yl (9Z,12E)-octadeca-9,12-dienoate × 5 AJP Digitonin × 1 LHG 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 1 Y01 CHOLESTEROL HEMISUCCINATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6VXO NaChBac-Nav1.7VSDII chimera in nanodisc Deposited 2020-02-22 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 817–832（16 aa）
Chain C 817–832（16 aa）
Chain D 817–832（16 aa）
Chain E 817–832（16 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 5 seconds before plunging
Resolution 3.50 Å
6W6O NaChBac-Nav1.7VSDII chimera and HWTX-IV complex Deposited 2020-03-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain A 817–832（16 aa）
Chain D 817–832（16 aa）
Chain F 817–832（16 aa）
Chain H 817–832（16 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 10
cryo-EM vitrification conditions Cryogen ETHANE；Blotted for 5 seconds before plunging
Resolution 3.20 Å
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 experimental conditions Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain A 739–779（41 aa）
Chain A 805–830（26 aa）
Chain B 739–779（41 aa）
Chain B 805–830（26 aa）
Chain C 739–779（41 aa）
Chain C 805–830（26 aa）
Chain D 739–779（41 aa）
Chain D 805–830（26 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 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
7W9K Cryo-EM structure of human Nav1.7-beta1-beta2 complex at 2.2 angstrom resolution Deposited 2021-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 3 Y01 CHOLESTEROL HEMISUCCINATE × 6 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 NA SODIUM ION × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 15 1PW (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
7W9L Cryo-EM structure of human Nav1.7(E406K)-beta1-beta2 complex Deposited 2021-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Mutation：E406K NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 3 Y01 CHOLESTEROL HEMISUCCINATE × 6 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 14 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7W9M Cryo-EM structure of human Nav1.7(E406K) in complex with auxiliary beta subunits, ProTx-II and tetrodotoxin (S6IV pi helix conformer) Deposited 2021-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Mutation：E406K 9SR (1R,5R,6R,7R,9S,11S,12S,13S,14S)-3-amino-14-(hydroxymethyl)-8,10-dioxa-2,4-diazatetracyclo[7.3.1.1~7,11~.0~1,6~]tetradec-3-ene-5,9,12,13,14-pentol (non-preferred name) × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 1 Y01 CHOLESTEROL HEMISUCCINATE × 5 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7W9P Cryo-EM structure of human Nav1.7(E406K) in complex with auxiliary beta subunits, huwentoxin-IV and saxitoxin (S6IV pi helix conformer) Deposited 2021-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Mutation：E406K 9SL [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 3 Y01 CHOLESTEROL HEMISUCCINATE × 6 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 13 1PW (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7W9T Cryo-EM structure of human Nav1.7(E406K) in complex with auxiliary beta subunits, huwentoxin-IV and saxitoxin (S6IV alpha helix conformer) Deposited 2021-12-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Mutation：E406K 9SL [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 2 Y01 CHOLESTEROL HEMISUCCINATE × 5 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 14 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7XM9 Cryo-EM structure of human NaV1.7/beta1/beta2-XEN907 Deposited 2022-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1977（1977 aa）
Mutation：W1150R NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 G2E (7~{R})-1'-pentylspiro[6~{H}-furo[3,2-f][1,3]benzodioxole-7,3'-indole]-2'-one × 1 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
7XMF Cryo-EM structure of human NaV1.7/beta1/beta2-Nav1.7-IN2 Deposited 2022-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1977（1977 aa）
Mutation：W1150R NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 G2W 3-[[4-[3-(4-fluoranyl-2-methyl-phenoxy)azetidin-1-yl]pyrimidin-2-yl]amino]-~{N}-methyl-benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.07 Å
7XMG Cryo-EM structure of human NaV1.7/beta1/beta2-TCN-1752 Deposited 2022-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1977（1977 aa）
Mutation：W1150R NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 G4I (1~{Z})-~{N}-[2-methyl-3-[(~{E})-[6-[4-[[4-(trifluoromethyloxy)phenyl]methoxy]piperidin-1-yl]-1~{H}-1,3,5-triazin-2-ylidene]amino]phenyl]ethanimidic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å
7XVE Human Nav1.7 mutant class-I Deposited 2022-05-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Mutation：E156K,G779R,L866F,T870M,A874F,V947F,M952F,V953F,V1438I,V1439F,G1454C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 Y01 CHOLESTEROL HEMISUCCINATE × 1 CLR CHOLESTEROL × 4 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 18 1PW (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 6 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7XVF Nav1.7 mutant class2 Deposited 2022-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Mutation：E156K,G779R,L866F,T870M,A874F,V947F,M952F,V953F,V1438I,V1439F,G1454C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 Y01 CHOLESTEROL HEMISUCCINATE × 5 CLR CHOLESTEROL × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 17 1PW (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 6 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8F0P Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the hybrid inhibitor GNE-1305 Deposited 2022-11-03 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 1501–1630（130 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 5 Y01 CHOLESTEROL HEMISUCCINATE × 1 X7L N-[6-(cyclopentylmethoxy)-1,3-benzothiazol-2-yl]-4-{[(1S,2S)-2-(dimethylamino)cyclohexyl]amino}-2-fluorobenzene-1-sulfonamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8F0Q Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the acylsulfonamide inhibitor GDC-0310 Deposited 2022-11-03 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 1501–1630（130 aa）
Not recorded BMA beta-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X7R 5-cyclopropyl-4-({1-[(1S)-1-(3,5-dichlorophenyl)ethyl]piperidin-4-yl}methoxy)-2-fluoro-N-(methanesulfonyl)benzamide × 1 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 5 Y01 CHOLESTEROL HEMISUCCINATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
8F0R Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the arylsulfonamide inhibitor GNE-3565 Deposited 2022-11-03 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 1501–1630（130 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 X7W 5-chloro-4-({(1S,2S,4S)-2-(dimethylamino)-4-[3-(trifluoromethyl)phenyl]cyclohexyl}amino)-2-fluoro-N-(pyrimidin-4-yl)benzene-1-sulfonamide × 1 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 2 Y01 CHOLESTEROL HEMISUCCINATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8F0S Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the hybrid inhibitor GNE-9296 Deposited 2022-11-03 Different construct Different mutation/modification 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 1501–1630（130 aa） Fragment：Chimeric construct of human Nav1.7 VSD4 and the NavPaS channel from American cockroach Periplaneta americana
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X80 5-chloro-4-(cyclopentylmethoxy)-N-(4-{[(1S,2S)-2-(dimethylamino)cyclohexyl]amino}-2-fluorobenzene-1-sulfonyl)-2-fluorobenzamide × 1 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 1 Y01 CHOLESTEROL HEMISUCCINATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8G1A Cryo-EM structure of Nav1.7 with CBD Deposited 2023-02-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 P0T cannabidiol × 2 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 2 Y01 CHOLESTEROL HEMISUCCINATE × 5 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 13 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8I5B Structure of human Nav1.7 in complex with bupivacaine Deposited 2023-01-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 1 Y01 CHOLESTEROL HEMISUCCINATE × 6 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 6 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 OJ0 Levobupivacaine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8I5G Structure of human Nav1.7 in complex with PF-05089771 Deposited 2023-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 Y01 CHOLESTEROL HEMISUCCINATE × 2 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 T70 PF-05089771 × 1 NA SODIUM ION × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 8 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8I5X Structure of human Nav1.7 in complex with Vinpocetine Deposited 2023-01-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 1 Y01 CHOLESTEROL HEMISUCCINATE × 5 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 T7F Vinpocetine × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 11 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8I5Y Structure of human Nav1.7 in complex with vixotrigine Deposited 2023-01-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 1 Y01 CHOLESTEROL HEMISUCCINATE × 4 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 TB4 Vixotrigine × 1 NA SODIUM ION × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 14 1PW (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8J4F Structure of human Nav1.7 in complex with Hardwickii acid Deposited 2023-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1988（1988 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 UK0 (4~{a}~{R},5~{S},6~{R},8~{a}~{R})-5-[2-(furan-3-yl)ethyl]-5,6,8~{a}-trimethyl-3,4,4~{a},6,7,8-hexahydronaphthalene-1-carboxylic acid × 1 Y01 CHOLESTEROL HEMISUCCINATE × 3 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 10 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8S9B Cryo-EM structure of Nav1.7 with LCM Deposited 2023-03-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 LQO lacosamide × 2 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 2 Y01 CHOLESTEROL HEMISUCCINATE × 4 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 8 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8S9C Cryo-EM structure of Nav1.7 with CBZ Deposited 2023-03-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 N6W benzo[b][1]benzazepine-11-carboxamide × 1 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 3 Y01 CHOLESTEROL HEMISUCCINATE × 5 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 9 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8THG Cryo-EM structure of Nav1.7 with RLZ Deposited 2023-07-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 657 6-(trifluoromethoxy)-1,3-benzothiazol-2-amine × 1 Y01 CHOLESTEROL HEMISUCCINATE × 3 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 6 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8THH Cryo-EM structure of Nav1.7 with LTG Deposited 2023-07-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 IYJ (6M)-6-(2,3-dichlorophenyl)-1,2,4-triazine-3,5-diamine × 2 Y01 CHOLESTEROL HEMISUCCINATE × 4 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 6 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 3 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8XMM Voltage-gated sodium channel Nav1.7 variant M9 Deposited 2023-12-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1988（1988 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CLR CHOLESTEROL × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 9 1PW (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 6 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
8XMN Voltage-gated sodium channel Nav1.7 variant M2 Deposited 2023-12-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å
8XMO Voltage-gated sodium channel Nav1.7 variant M4 Deposited 2023-12-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1988（1988 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 7 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
8YHZ The co-crystal structure of the Fab fragment of Ab-1080 with NaV1.7 VSDII peptide Deposited 2024-02-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain P 764–774（11 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2M potassium thiocyanate, 25% W/V Polyethylene glycol 3,350
Resolution 1.62 Å R-free 0.210
9ITI Nav1.7 with mutations that eliminate beta1 binding Deposited 2024-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1988（1988 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 2 NA SODIUM ION × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 10 1PW (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 Y01 CHOLESTEROL HEMISUCCINATE × 4 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.92 Å

42 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SCN9A_HUMAN
Isoform Q15858-3
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 44–74； UniProt 747–777 Author chain A； PDBConstruct 96–127； UniProt 811–842 Author chain B； PDBConstruct 44–74； UniProt 747–777 Author chain B； PDBConstruct 96–127； UniProt 811–842 Author chain C； PDBConstruct 44–74； UniProt 747–777 Author chain C； PDBConstruct 96–127； UniProt 811–842 Author chain D； PDBConstruct 44–74； UniProt 747–777 Author chain D； PDBConstruct 96–127； UniProt 811–842

Beta/omega-theraphotoxin-Tp2a

OrganismNot specified

UniProt P83476

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count Chain E； UniProt 1–30 Chain F； UniProt 1–30 Chain G； UniProt 1–30 Chain H； UniProt 1–30 Not recorded Nav1.7 VSD2-NavAb chimera × 4 （A8EVM5,Q15858） Fab light chain × 2 Fab heavy chain × 2 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

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 6N4Q Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2N9T NMR solution structure of ProTx-II Deposited 2015-12-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–30（30 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions 298 K；Pressure ambient
NMR sample composition 2 mg protein, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 2 mg protein, 100% D2O | 100% D2O
Resolution not provided
5O0U Crystal structure of tarantula venom peptide Protoxin-II Deposited 2017-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–30（30 aa）
Not recorded CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2M lithium sulfate, 100 mM Tris-HCl (pH 8), 2% v/v PEG 400
Resolution 0.99 Å R-free 0.140
6MK4 Solution NMR structure of spider toxin analogue [E17K]ProTx-II Deposited 2018-09-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–30（30 aa）
Mutation：E17K No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions 298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR measurement conditions 298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition 2 mg/mL [E17K]ProTx-II, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6N4I Structural basis of Nav1.7 inhibition by a gating-modifier spider toxin Deposited 2018-11-19 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 1–30（30 aa）
Chain F 1–30（30 aa）
Chain G 1–30（30 aa）
Chain H 1–30（30 aa）
Not recorded 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；2.3-2.6M Ammonium sulfate, 100 mM HEPES, pH 7.0; 30% sucrose for cryo
Resolution 3.54 Å R-free 0.294
6N4R CryoEM structure of Nav1.7 VSD2 (deactived state) in complex with the gating modifier toxin ProTx2 Deposited 2018-11-20 Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric
Chain E 1–30（30 aa）
Chain F 1–30（30 aa）
Chain G 1–30（30 aa）
Chain H 1–30（30 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

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TXPR2_THRPR
Isoform —
PDB entities 2
Chains and sequence ranges Author chain E； PDBConstruct 1–30； UniProt 1–30 Author chain F； PDBConstruct 1–30； UniProt 1–30 Author chain G； PDBConstruct 1–30； UniProt 1–30 Author chain H； PDBConstruct 1–30； UniProt 1–30

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 6n4q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6n4q
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6n4q
Deposition date deposition_date2018-11-20
Structure title titleCryoEM structure of Nav1.7 VSD2 (actived state) in complex with the gating modifier toxin ProTx2
Keywords keywordsvoltage-gated sodium channel, gating modifier toxin, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier49.87 Å
Radius of gyration Rg (electron density) rg_electron49.19 Å
Forward intensity I(0) i0711812000.00
Molecular weight molecular_weight232500.0 kDa
Excluded volume excluded_volume295610 ų
Envelope volume envelope_volume452390 ų
Hydration-shell volume shell_volume78439 ų
Envelope diameter envelope_diameter193.3 Å
Shell Rg shell_rg51.67 Å
Envelope Rg envelope_rg48.80 Å
Shape Rg shape_rg49.15 Å
Total Rg total_rg49.43 Å
Total atoms total_atoms16358
Residues n_residues2052
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax179.6 Å
Rg (real space) rg_real49.99 Å
Rg uncertainty (real space) rg_real_error2.09 Å
I(0) (real space) i0_real7.1180e+08
I(0) uncertainty (real space) i0_real_error1.4040e+07
Rg (reciprocal space) rg_reciprocal49.87 Å
I(0) (reciprocal space) i0_reciprocal711700000.0000
Solution quality estimate total_estimate0.8358
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary61.7 Å
Skewness Skewness skewness0.478
Kurtosis Kurtosis kurtosis0.259
Angular range angular_range— – 0.1600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha43680000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.666; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.863
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id6n4qI01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6n4qI02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6n4qJ02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6n4qK01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6n4qK02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6n4qL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)