6vrr

Crystal structure of a disease mutant of the Voltage-gated Sodium Channel Beta 2 subunit extracellular domain

Method: X-RAY DIFFRACTION D_max: 63.3 Å Quality: GOOD

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

Sodium channel subunit beta-2

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 30–153	Mutation：R137H	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M HEPES (pH 7.0), 14% PEG 6000	Resolution 1.45 Å R-free 0.183

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 6VRR	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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 30–148（119 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 30–148（119 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
5FDY Crystal structure of the Voltage-gated Sodium Channel Beta 2 subunit extracellular domain, C72A/C75A mutant Deposited 2015-12-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–153（124 aa） Fragment：UNP residues 30-153	Mutation：C55A, C72A, C75A	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；PEG 6000	Resolution 1.85 Å R-free 0.185
5FDY Crystal structure of the Voltage-gated Sodium Channel Beta 2 subunit extracellular domain, C72A/C75A mutant Deposited 2015-12-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 30–153（124 aa） Fragment：UNP residues 30-153	Mutation：C55A, C72A, C75A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；PEG 6000	Resolution 1.85 Å R-free 0.185
5FEB Crystal structure of the Voltage-gated Sodium Channel Beta 2 subunit extracellular domain Deposited 2015-12-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–151（122 aa） Fragment：UNP residues 30-151	Mutation：C55A	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；PEG 6000	Resolution 1.35 Å R-free 0.206
6J8E Human Nav1.2-beta2-KIIIA ternary complex Deposited 2019-01-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 27–148（122 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 NA SODIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 5.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 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
7W77 cryo-EM structure of human NaV1.3/beta1/beta2-bulleyaconitineA Deposited 2021-12-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 3 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 16 966 [(1S,2R,3R,4R,5R,6S,8R,9S,13S,16S,17R,18R)-11-ethyl-5-hydroxy-6,16,18-trimethoxy-4-(4-methoxybenzoyl)-13-(methoxymethyl)-11-azahexacyclo[7.7.2.12,5.01,10.03,8.013,17]nonadecan-8-yl] acetate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7W7F Cryo-EM structure of human NaV1.3/beta1/beta2-ICA121431 Deposited 2021-12-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 17 8DE 2,2-diphenyl-~{N}-[4-(1,3-thiazol-2-ylsulfamoyl)phenyl]ethanamide × 1 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 3.35 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 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 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 aa）	Not recorded	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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 aa）	Not recorded	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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 aa）	Not recorded	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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 aa）	Not recorded	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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 aa）	Not recorded	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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–215（215 aa）	Not recorded	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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 aa）	Not recorded	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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 aa）	Not recorded	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
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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 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
8GZ1 Cryo-EM structure of human NaV1.6/beta1/beta2,apo state Deposited 2022-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NA SODIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8GZ2 Cryo-EM structure of human NaV1.6/beta1/beta2-4,9-anhydro-tetrodotoxin Deposited 2022-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 WMK (1R,2S,3S,4R,5R,9S,11S,12S,14R)-7-amino-2,4,12-trihydroxy-2-(hydroxymethyl)-10,13,15-trioxa-6,8-diazapentacyclo[7.4.1.1~3,12~.0~5,11~.0~5,14~]pentadec-7-en-8-ium (non-preferred name) × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 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
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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 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
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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–215（215 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

34 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SCN2B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–127； UniProt 30–153

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6vrr
Deposition date deposition_date	2020-02-09
Structure title title	Crystal structure of a disease mutant of the Voltage-gated Sodium Channel Beta 2 subunit extracellular domain
Keywords keywords	Sodium Channel, Beta sub-unit, SCN2B, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	16.44 Å
Radius of gyration Rg (electron density) rg_electron	15.27 Å
Forward intensity I(0) i0	4708640.00
Molecular weight molecular_weight	14915.0 kDa
Excluded volume excluded_volume	18380 Å³
Envelope volume envelope_volume	21178 Å³
Hydration-shell volume shell_volume	12218 Å³
Envelope diameter envelope_diameter	61.7 Å
Shell Rg shell_rg	20.85 Å
Envelope Rg envelope_rg	16.06 Å
Shape Rg shape_rg	15.23 Å
Total Rg total_rg	16.42 Å
Total atoms total_atoms	2042
Residues n_residues	127
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	63.3 Å
Rg (real space) rg_real	16.47 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	4.7090e+06
I(0) uncertainty (real space) i0_real_error	6.0970e+04
Rg (reciprocal space) rg_reciprocal	16.47 Å
I(0) (reciprocal space) i0_reciprocal	4709000.0000
Solution quality estimate total_estimate	0.8005
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.7 Å
Skewness Skewness skewness	0.449
Kurtosis Kurtosis kurtosis	0.038
Angular range angular_range	— – 0.4850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	888700.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.518; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.850; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Sodium channel subunit beta-2
Molecular weight formula_weight	14768.7 kDa
Mutation mutation	R137H
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2643

SNAMEVTVPATLNVLNGSDARLPCTFNSAYTVNHKQFSLNWTYQECNNCSEEMFLQFRMKIINLKLERFQDRVEFSGNPSKYDVSVMLRNVQPEDEGIYNCYIMNPPDRHHGHGKIHLQVLMEEPPE

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	166

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6vrra1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6vrra2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

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8. Citations (1)

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Unit-cell length a length_a	40.271 Å
Unit-cell length b length_b	53.582 Å
Unit-cell length c length_c	59.319 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	39.760 Å
R factor r_factor	0.1516
R_work r_work	0.1499
R_free r_free	0.1827

fit	/app/data/saxs_computation/vr/6vrr/6vrr.fit
pddf	/app/data/pr_computation/vr/6vrr/6vrr.pr.out
profile	/app/data/saxs_computation/vr/6vrr/6vrr.dat