SAXSdb — 6n4r

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

Nav1.7 VSD2-NavAb chimera

Arcobacter butzleri (strain RM4018)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 12	Beta/omega-theraphotoxin-Tp2a × 4 （P83476） Fab light chain × 2 Fab heavy chain × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A8EVM5_ARCB4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 19–43； UniProt 1–25 Author chain A； PDBConstruct 75–95； UniProt 58–78 Author chain A； PDBConstruct 128–288； UniProt 107–267 Author chain B； PDBConstruct 19–43； UniProt 1–25 Author chain B； PDBConstruct 75–95； UniProt 58–78 Author chain B； PDBConstruct 128–288； UniProt 107–267 Author chain C； PDBConstruct 19–43； UniProt 1–25 Author chain C； PDBConstruct 75–95； UniProt 58–78 Author chain C； PDBConstruct 128–288； UniProt 107–267 Author chain D； PDBConstruct 19–43； UniProt 1–25 Author chain D； PDBConstruct 75–95； UniProt 58–78 Author chain D； PDBConstruct 128–288； UniProt 107–267

Nav1.7 VSD2-NavAb chimera

Arcobacter butzleri (strain RM4018)

UniProt Q15858

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 12	Beta/omega-theraphotoxin-Tp2a × 4 （P83476） Fab light chain × 2 Fab heavy chain × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

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

Beta/omega-theraphotoxin-Tp2a

OrganismNot specified

UniProt P83476

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 12	Nav1.7 VSD2-NavAb chimera × 4 （A8EVM5,Q15858） Fab light chain × 2 Fab heavy chain × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

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

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6n4r
Deposition date deposition_date	2018-11-20
Structure title title	CryoEM structure of Nav1.7 VSD2 (deactived state) in complex with the gating modifier toxin ProTx2
Keywords keywords	voltage-gated sodium channel, gating modifier toxin, 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.

6n4r__assembly_1__model_1

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

Download this curve (.dat)

6n4r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6n4r__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	47.08 Å
Rg (electron density)	46.37 Å
Total Rg	46.80 Å
Atom count	15444
Residues	1942
Excluded volume	279500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6n4r__assembly_1__model_1`	dodecameric （12）	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 (4)

Entity 1 Entity 1 polymer

Description description	Nav1.7 VSD2-NavAb chimera
Molecular weight formula_weight	33453.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C,D,A
Atom count atom_count	15444

MDYKDDDDKGSLVPRGSHMYLRITNIVESSFFTKFIIYLIVLNTLFMAMEHHPMTEEFKNVLAIGNLVFTGIFAIEIILRIYVHRISFFKDPWSLFDSLIVTLSLVELFLADVEGLSVLRSFRLLRVFRLVTAVPQMRKIVSALISVIPGMLSVIALMTLFFYIFAIMATQLFGERFPEWFGTLGESFYTLFQVMTLESWSMGIVRPLMEVYPYAWVFFIPFIFVVTFVMINLVVAICVDAMAILNQKEEQHIIDEVQSHEDNINNEIIKLREEIVELKELIKTSLKN

Source Source

Source organism organism	Arcobacter butzleri (strain RM4018)
NCBI taxonomy ID ncbi_taxonomy_id	367737
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Beta/omega-theraphotoxin-Tp2a
Molecular weight formula_weight	3839.7 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

YCQKWMWTCDSERKCCEGMVCRLWCKKKLW

Entity 3 Entity 3 polymer

Description description	Fab light chain
Molecular weight formula_weight	23483.9 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,K

EIVLTQSPALMAASPGEKVTITCSVSLSISSSNLFWYQQKSETSPKPWIYGTSKLASGVPVRFSGSGSGTSYSLTISSMEAEDAATYYCQQWSSHSFTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Entity 4 Entity 4 polymer

Description description	Fab heavy chain
Molecular weight formula_weight	24523.5 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,L

EVQLVESGGGLVKPGGSLKLSCAASGFTFSNYAMSWVRQTPEKRLEWVATISNGGRYTYYPDSVKGRFTISRDNAKNSLYLQMSSLRSEDTAMYYCARHLYRYDVGGALDYWGQGTSVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPTIKP

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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	4.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	53206

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

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

Nav1.7 VSD2-NavAb chimera

State in the Current Structure

Other States of the Same Protein in the Database

Nav1.7 VSD2-NavAb chimera

State in the Current Structure

Other States of the Same Protein in the Database

Beta/omega-theraphotoxin-Tp2a

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

6n4r__assembly_1__model_1

6n4r__assembly_1__model_1 | I(q)

6n4r__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

7. Citations (1)

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

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

Nav1.7 VSD2-NavAb 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

Nav1.7 VSD2-NavAb 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/omega-theraphotoxin-Tp2a

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

6n4r__assembly_1__model_1

6n4r__assembly_1__model_1 | I(q)

6n4r__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

7. Citations (1)