6nt4

Cryo-EM structure of a human-cockroach hybrid Nav channel bound to alpha-scorpion toxin AaH2.

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,Sodium channel protein PaFPC1

Periplaneta americana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3 其他Polymer 1	Alpha-mammal toxin AaH2 × 2 （P01484） ;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 × 5 (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 Digitonin × 1 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 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 55–1208； UniProt 1–1154 Author chain A； PDBConstruct 1341–1559； UniProt 1287–1505

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

Periplaneta americana

UniProt Q15858

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3 其他Polymer 1	Alpha-mammal toxin AaH2 × 2 （P01484） ;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 × 5 (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 Digitonin × 1 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 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 1209–1340； UniProt 1500–1631

Alpha-mammal toxin AaH2

OrganismNot specified

UniProt P01484

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3 其他Polymer 1	Sodium channel protein PaFPC1,Sodium channel protein type 9 subunit alpha,Sodium channel protein PaFPC1 × 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 × 5 (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 Digitonin × 1 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE × 1 CHOLESTEROL HEMISUCCINATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SCX2_ANDAU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–64； UniProt 20–83 Author chain C； PDBConstruct 1–64； UniProt 20–83

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	6nt4
Deposition date deposition_date	2019-01-28
Structure title title	Cryo-EM structure of a human-cockroach hybrid Nav channel bound to alpha-scorpion toxin AaH2.
Keywords keywords	Sodium channel, scorpion toxin, electrical signaling, fast inactivation, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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.

6nt4__assembly_1__model_1

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

Download this curve (.dat)

6nt4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6nt4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.84 Å
Rg (electron density)	39.67 Å
Total Rg	40.12 Å
Atom count	11924
Residues	1406
Excluded volume	217590 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6nt4__assembly_1__model_1`	trimeric （3）	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,Sodium channel protein PaFPC1
Molecular weight formula_weight	178763.7 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	11924

WSHPQFEKGGGSGGGSGGSAWSHPQFEKGGSGGDYKDDDDKGGSGGDYKDDDDKMADNSPLIREERQRLFRPYTRAMLTAPSAQPAKENGKTEENKDNSRDKGRGANKDRDGSAHPDQALEQGSRLPARMRNIFPAELASTPLEDFDPFYKNKKTFVVVTKAGDIFRFSGEKSLWMLDPFTPIRRVAISTMVQPIFSYFIMITILIHCIFMIMPATQTTYILELVFLSIYTIEVVVKVLARGFILHPFAYLRDPWNWLDFLVTLIGYITLVVDLGHLYALRAFRVLRSWRTVTIVPGWRTIVDALSLSITSLKDLVLLLLFSLSVFALIGLQLFMGNLKHKCVKHFPADGSWGNFTDERWFNYTSNSSHWYIPDDWIEYPLCGNSSGAGMCPPGYTCLQGYGGNPNYGYTSFDTFGWAFLSVFRLVTLDYWEDLYQLALRSAGPWHILFFIIVVFYGTFCFLNFILAVVVMSYTHMVKRADEEKAAERELKKEKKAASVANNTANGQEQTTIEMNGDEAVVIDNNDQAARQQSDPETPAPSVTQRLTDFLCVWDCCVPWQKLQGAIGAVVLSPFFELFIAVIIVLNITFMALDHHDMNIEFERILRTGNYIFTSIYIVEAVLKIIALSPKFYFKDSWNVFDFIIVVFAILELGLEGVQGLSVFRSFRLLRVFRLAKFWPTLNNFMSVMTKSYGAFVNVMYVMFLLLFIFAIIGMQLFGMNYIDNMERFPDGDLPRWNFTDFLHSFMIVFRALCGEWIESMWDCMLVGDWSCIPFFVAVFFVGNLVILNLLIALLLNNYGSFCTSPTSDEEDSKDEDALAQIVRIFKRFKPNLNAVKLSPMKPDSEDIVESQEIQGNNIADAEDVLAGEFPPDCCCNAFYKCFPSRPARDSSVQRMWSNIRRVCFLLAKNKYFQKFVTAVLVITSVLLALEDIYLPQRPVLVNITLYVDYVLTAFFVIEMIIMLFAVGFKKYFTSKWYWLDFIVVVAYLLNFVLMCAGIEALQTLRLLRVFRLFRPLSKVNGMQVVTSTLVEAVPHIFNVILVGIFFWLVFAIMGVQLFAGKFYKCVDENSTVLSHEITMDRNDCLHENYTWENSPMNFDHVGNAYLSLLQVATFKGWLQIMNDAIDSREVHKQPIRETNIYMYLYFIFFIVFGSFFILKLFVCILIDIFRQQRRKAEGLSATDSRTQLIYRRAVMRTMSAKPVKRIPKPGNKIQGCIFDLVTNQAFDISIMVLICLNMVTMMVEKEGQSQHMTEVLYWINVVFIILFTGECVLKLISLRHYYFTVGWNIFDFVVVIISIVGMFLADLIETYFVSPTLFRVIRLARIGRILRLVKGAKGIRLLLLALRKALRTLFNVSFLLFVIMFVYAVFGMEFFMHIRDAGAIDDVYNFKTFGQSIILLFQLATSAGWDGVYFAIANEEDCRAPDHELGYPGNCGSRALGIAYLVSYLIITCLVVINMYAAVILDYVLEVYEDSKEGLTDDDYDMFFEVWQQFDPEATQYIRYDQLSELLEALQPPLQVQKPNKYKILSMNIPICKDDHIFYKDVLEALVKDVFSRRG

Source Source

Source organism organism	Periplaneta americana
Common name common_name	American cockroach
NCBI taxonomy ID ncbi_taxonomy_id	6978
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Alpha-mammal toxin AaH2
Molecular weight formula_weight	7260.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C

VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYKLPDHVRTKGPGRCHX

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 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	(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
Molecular weight formula_weight	742.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	Digitonin
Molecular weight formula_weight	1229.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
Molecular weight formula_weight	723.0 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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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6nt4B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	30 — Defensin A-like
Homologous superfamily homologous superfamily	10 — Knottin, scorpion toxin-like

Domain ID domain_id	6nt4C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	30 — Defensin A-like
Homologous superfamily homologous superfamily	10 — Knottin, scorpion toxin-like

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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	1

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

Resolution resolution	3.50 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	251714

Cryo-EM structure of a human-cockroach hybrid Nav channel bound to alpha-scorpion toxin AaH2.

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

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

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,Sodium channel protein PaFPC1

State in the Current Structure

Other States of the Same Protein in the Database

Alpha-mammal toxin AaH2

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

6nt4__assembly_1__model_1

6nt4__assembly_1__model_1 | I(q)

6nt4__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

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Cryo-EM structure of a human-cockroach hybrid Nav channel bound to alpha-scorpion toxin AaH2.

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

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

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,Sodium channel protein PaFPC1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Alpha-mammal toxin AaH2

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

6nt4__assembly_1__model_1

6nt4__assembly_1__model_1 | I(q)

6nt4__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

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)