8f0s

Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the hybrid inhibitor GNE-9296

Method: ELECTRON MICROSCOPY

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

Sodium channel protein PaFPC1,Sodium channel protein type 9 subunit alpha chimera

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2 其他Polymer 2	Beta-diguetoxin-Dc1a × 1 （P49126） ;beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 5-chloro-4-(cyclopentylmethoxy)-N-(4-{[(1S,2S)-2-(dimethylamino)cyclohexyl]amino}-2-fluorobenzene-1-sulfonyl)-2-fluorobenzamide × 1 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 1 CHOLESTEROL HEMISUCCINATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SCNA1_PERAM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 56–1210； UniProt 1–1155 Author chain A； PDBConstruct 1341–1608； UniProt 1286–1553

Sodium channel protein PaFPC1,Sodium channel protein type 9 subunit alpha chimera

Homo sapiens

UniProt Q15858

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2 其他Polymer 2	Beta-diguetoxin-Dc1a × 1 （P49126） ;beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 5-chloro-4-(cyclopentylmethoxy)-N-(4-{[(1S,2S)-2-(dimethylamino)cyclohexyl]amino}-2-fluorobenzene-1-sulfonyl)-2-fluorobenzamide × 1 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 1 CHOLESTEROL HEMISUCCINATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SCN9A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1211–1340； UniProt 1501–1630

Beta-diguetoxin-Dc1a

Diguetia canities

UniProt P49126

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2 其他Polymer 2	Sodium channel protein PaFPC1,Sodium channel protein type 9 subunit alpha chimera × 1 （D0E0C2,Q15858） ;beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 5-chloro-4-(cyclopentylmethoxy)-N-(4-{[(1S,2S)-2-(dimethylamino)cyclohexyl]amino}-2-fluorobenzene-1-sulfonyl)-2-fluorobenzamide × 1 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 1 CHOLESTEROL HEMISUCCINATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TXI92_DIGCA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 16–71； UniProt 39–94

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8f0s
Deposition date deposition_date	2022-11-03
Last revision last_revision	2023-04-12
Structure title title	Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the hybrid inhibitor GNE-9296
Keywords keywords	Ion channel, small molecule, inhibitor, MEMBRANE PROTEIN-INHIBITOR complex; MEMBRANE PROTEIN/INHIBITOR
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8f0s__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8f0s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8f0s__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	35.89 Å
Rg (electron density)	35.02 Å
Total Rg	35.67 Å
Atom count	9734
Residues	1158
Excluded volume	178230 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8f0s__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Sodium channel protein PaFPC1,Sodium channel protein type 9 subunit alpha chimera
Molecular weight formula_weight	184481.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9734

MWSHPQFEKGGGSGGGSGGSAWSHPQFEKGGSGGDYKDDDDKGGSGGDYKDDDDKMADNSPLIREERQRLFRPYTRAMLTAPSAQPAKENGKTEENKDNSRDKGRGANKDRDGSAHPDQALEQGSRLPARMRNIFPAELASTPLEDFDPFYKNKKTFVVVTKAGDIFRFSGEKSLWMLDPFTPIRRVAISTMVQPIFSYFIMITILIHCIFMIMPATQTTYILELVFLSIYTIEVVVKVLARGFILHPFAYLRDPWNWLDFLVTLIGYITLVVDLGHLYALRAFRVLRSWRTVTIVPGWRTIVDALSLSITSLKDLVLLLLFSLSVFALIGLQLFMGNLKHKCVKHFPADGSWGNFTDERWFNYTSNSSHWYIPDDWIEYPLCGNSSGAGMCPPGYTCLQGYGGNPNYGYTSFDTFGWAFLSVFRLVTLDYWEDLYQLALRSAGPWHILFFIIVVFYGTFCFLNFILAVVVMSYTHMVKRADEEKAAERELKKEKKAASVANNTANGQEQTTIEMNGDEAVVIDNNDQAARQQSDPETPAPSVTQRLTDFLCVWDCCVPWQKLQGAIGAVVLSPFFELFIAVIIVLNITFMALDHHDMNIEFERILRTGNYIFTSIYIVEAVLKIIALSPKFYFKDSWNVFDFIIVVFAILELGLEGVQGLSVFRSFRLLRVFRLAKFWPTLNNFMSVMTKSYGAFVNVMYVMFLLLFIFAIIGMQLFGMNYIDNMERFPDGDLPRWNFTDFLHSFMIVFRALCGEWIESMWDCMLVGDWSCIPFFVAVFFVGNLVILNLLIALLLNNYGSFCTSPTSDEEDSKDEDALAQIVRIFKRFKPNLNAVKLSPMKPDSEDIVESQEIQGNNIADAEDVLAGEFPPDCCCNAFYKCFPSRPARDSSVQRMWSNIRRVCFLLAKNKYFQKFVTAVLVITSVLLALEDIYLPQRPVLVNITLYVDYVLTAFFVIEMIIMLFAVGFKKYFTSKWYWLDFIVVVAYLLNFVLMCAGIEALQTLRLLRVFRLFRPLSKVNGMQVVTSTLVEAVPHIFNVILVGIFFWLVFAIMGVQLFAGKFYKCVDENSTVLSHEITMDRNDCLHENYTWENSPMNFDHVGNAYLSLLQVATFKGWLQIMNDAIDSREVHKQPIRETNIYMYLYFIFFIVFGSFFILKLFVCILIDIFRQQRRKAEGLSATDSRTQLIYRRAVMRTMSAKPVKRIPKPGNKIQGCIFDLVTNQAFDISIMVLICLNMVTMMVEKEGQSQHMTEVLYWINVVFIILFTGECVLKLISLRHYYFTVGWNIFDFVVVIISIVGMFLADLIETYFVSPTLFRVIRLARIGRILRLVKGAKGIRLLLLALRKALRTLFNVSFLLFVIMFVYAVFGMEFFMHIRDAGAIDDVYNFKTFGQSIILLFQLATSAGWDGVYFAIANEEDCRAPDHELGYPGNCGSRALGIAYLVSYLIITCLVVINMYAAVILDYVLEVYEDSKEGLTDDDYDMFFEVWQQFDPEATQYIRYDQLSELLEALQPPLQVQKPNKYKILSMNIPICKDDHIFYKDVLEALVKDVFSRRGSPVEAGDVQAPNVDEAEYKPVSSTLQRQREEYCVRLIQNAWRKHKQQN

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Beta-diguetoxin-Dc1a
Molecular weight formula_weight	8240.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

HHHHHHGENLYFQGSAKDGDVEGPAGCKKYDVECDSGECCQKQYLWYKWRPLDCRCLKSGFFSSKCVCRDV

Source Source

Source organism organism	Diguetia canities
NCBI taxonomy ID ncbi_taxonomy_id	38407
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 branched

Description description	;beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	910.8 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	5-chloro-4-(cyclopentylmethoxy)-N-(4-{[(1S,2S)-2-(dimethylamino)cyclohexyl]amino}-2-fluorobenzene-1-sulfonyl)-2-fluorobenzamide
Molecular weight formula_weight	570.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
Molecular weight formula_weight	744.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	CHOLESTEROL HEMISUCCINATE
Molecular weight formula_weight	486.7 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.10 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	826525

Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the hybrid inhibitor GNE-9296

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

Sodium channel protein PaFPC1,Sodium channel protein type 9 subunit alpha chimera

State in the Current Structure

Other States of the Same Protein in the Database

Sodium channel protein PaFPC1,Sodium channel protein type 9 subunit alpha chimera

State in the Current Structure

Other States of the Same Protein in the Database

Beta-diguetoxin-Dc1a

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8f0s__assembly_1__model_1

8f0s__assembly_1__model_1 | I(q)

8f0s__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

7. Citations (1)

Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the hybrid inhibitor GNE-9296

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

Sodium channel protein PaFPC1,Sodium channel protein type 9 subunit alpha chimera

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Sodium channel protein PaFPC1,Sodium channel protein type 9 subunit alpha chimera

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Beta-diguetoxin-Dc1a

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8f0s__assembly_1__model_1

8f0s__assembly_1__model_1 | I(q)

8f0s__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

7. Citations (1)