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6vxo

NaChBac-Nav1.7VSDII chimera in nanodisc

Method: ELECTRON MICROSCOPY Dmax: 107.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

NaChBac-Nav1.7VSDII chimera

Bacillus halodurans C-125

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 Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 817–832 Chain C； UniProt 817–832 Chain D； UniProt 817–832 Chain E； UniProt 817–832 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

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 6VXO 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 mutation/modification 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
6N4Q CryoEM structure of Nav1.7 VSD2 (actived state) in complex with the gating modifier toxin ProTx2 Deposited 2018-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 3.60 Å
6N4R CryoEM structure of Nav1.7 VSD2 (deactived state) in complex with the gating modifier toxin ProTx2 Deposited 2018-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 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
6W6O NaChBac-Nav1.7VSDII chimera and HWTX-IV complex Deposited 2020-03-17 Different oligomeric state 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 ligand/ion Different experimental conditions Different structure-quality metrics 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 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 ligand/ion 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 —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 98–113； UniProt 817–832 Author chain C； PDBConstruct 98–113； UniProt 817–832 Author chain D； PDBConstruct 98–113； UniProt 817–832 Author chain E； PDBConstruct 98–113； UniProt 817–832

NaChBac-Nav1.7VSDII chimera

Bacillus halodurans C-125

UniProt Q9KCR8

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 Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–97 Chain A； UniProt 111–274 Chain C； UniProt 1–97 Chain C； UniProt 111–274 Chain D； UniProt 1–97 Chain D； UniProt 111–274 Chain E； UniProt 1–97 Chain E； UniProt 111–274 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

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 6VXO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6VWX NaChBac in lipid nanodisc Deposited 2020-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–274（274 aa）
Chain D 1–274（274 aa）
Chain E 1–274（274 aa）
Chain F 1–274（274 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 NA SODIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；blot for 5 seconds before plunging
Resolution 3.10 Å
6VX3 NaChBac in GDN Deposited 2020-02-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–274（274 aa）
Chain B 1–274（274 aa）
Chain C 1–274（274 aa）
Chain D 1–274（274 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 10
cryo-EM vitrification conditions Cryogen ETHANE；blot for 5 seconds before plunging
Resolution 3.70 Å
6W6O NaChBac-Nav1.7VSDII chimera and HWTX-IV complex Deposited 2020-03-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–97（97 aa）
Chain A 111–274（164 aa）
Chain D 1–97（97 aa）
Chain D 111–274（164 aa）
Chain F 1–97（97 aa）
Chain F 111–274（164 aa）
Chain H 1–97（97 aa）
Chain H 111–274（164 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

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q9KCR8_BACHD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–97； UniProt 1–97 Author chain A； PDBConstruct 114–277； UniProt 111–274 Author chain C； PDBConstruct 1–97； UniProt 1–97 Author chain C； PDBConstruct 114–277； UniProt 111–274 Author chain D； PDBConstruct 1–97； UniProt 1–97 Author chain D； PDBConstruct 114–277； UniProt 111–274 Author chain E； PDBConstruct 1–97； UniProt 1–97 Author chain E； PDBConstruct 114–277； UniProt 111–274

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 6vxo

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6vxo
Deposition date deposition_date2020-02-22
Structure title titleNaChBac-Nav1.7VSDII chimera in nanodisc
Keywords keywordsNaChBac, Channels; Sodium Ion-Selective, 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_guinier34.70 Å
Radius of gyration Rg (electron density) rg_electron33.25 Å
Forward intensity I(0) i0131900000.00
Molecular weight molecular_weight113670.0 kDa
Excluded volume excluded_volume151650 ų
Envelope volume envelope_volume193730 ų
Hydration-shell volume shell_volume48161 ų
Envelope diameter envelope_diameter116.1 Å
Shell Rg shell_rg40.16 Å
Envelope Rg envelope_rg33.59 Å
Shape Rg shape_rg33.23 Å
Total Rg total_rg33.99 Å
Total atoms total_atoms8048
Residues n_residues904
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 dmax107.6 Å
Rg (real space) rg_real34.55 Å
Rg uncertainty (real space) rg_real_error0.68 Å
I(0) (real space) i0_real1.3190e+08
I(0) uncertainty (real space) i0_real_error2.1290e+06
Rg (reciprocal space) rg_reciprocal34.64 Å
I(0) (reciprocal space) i0_reciprocal131900000.0000
Solution quality estimate total_estimate0.8886
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary46.8 Å
Skewness Skewness skewness0.169
Kurtosis Kurtosis kurtosis-0.334
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11930000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.865
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id6vxoA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily350 — Voltage-gated potassium channels. Chain C
Domain ID domain_id6vxoA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70 —
Domain ID domain_id6vxoC01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily350 — Voltage-gated potassium channels. Chain C
Domain ID domain_id6vxoC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70 —
Domain ID domain_id6vxoD01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily350 — Voltage-gated potassium channels. Chain C
Domain ID domain_id6vxoD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70 —
Domain ID domain_id6vxoE01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily350 — Voltage-gated potassium channels. Chain C
Domain ID domain_id6vxoE02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70 —
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8. Citations (1)

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9. Files and Curves (10)