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6n4q

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

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nav1.7 VSD2-NavAb chimera

Arcobacter butzleri (strain RM4018)

UniProt A8EVM5

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

Monomer

None

Homodimer

None

Homotetramer
24js 24jt 24ju 3rvy 3rvz 3rw0 4ekw 4ekw 4ms2 4mtf 4mtg 4mto

69 assemblies; showing the first 12

Other homooligomers

None

Heteromeric or nucleic-acid complex
5ek0 6n4q 6n4r 6p6w 7k48

5 assemblies

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

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
21tp 21tq 5ek0 6j8g 6j8h 6j8i 6j8j 6n4q 6n4r 6nt3 6nt4 6vxo

43 assemblies; showing the first 12

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

Monomer
2n9t 5o0u 6mk4

3 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
6n4i 6n4q 6n4r

3 assemblies

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_id6n4q
Deposition date deposition_date2018-11-20
Structure title titleCryoEM structure of Nav1.7 VSD2 (actived state) in complex with the gating modifier toxin ProTx2
Keywords keywordsvoltage-gated sodium channel, gating modifier toxin, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON 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.

6n4q__assembly_1__model_1

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

Download this curve (.dat)

6n4q__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6n4q__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）49.87 Å
Rg (electron density)49.19 Å
Total Rg49.43 Å
Atom count16358
Residues2052
Excluded volume295610 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6n4q__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)

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id6n4qI01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6n4qI02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6n4qJ02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6n4qK01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6n4qK02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6n4qL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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7. Citations (1)