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6n4i

Structural basis of Nav1.7 inhibition by a gating-modifier spider toxin

Method: X-RAY DIFFRACTION Dmax: 126.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Beta/omega-theraphotoxin-Tp2a

Thrixopelma pruriens

UniProt P83476

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 heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain E； UniProt 1–30 Chain F； UniProt 1–30 Chain G； UniProt 1–30 Chain H； UniProt 1–30 Not recorded Nav1.7 VSD2-NavAb channel chimera protein × 4 6OU [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate × 16 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；2.3-2.6M Ammonium sulfate, 100 mM HEPES, pH 7.0; 30% sucrose for cryo Resolution 3.54 Å R-free 0.294

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 6N4I Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2N9T NMR solution structure of ProTx-II Deposited 2015-12-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–30（30 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions 298 K；Pressure ambient
NMR sample composition 2 mg protein, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 2 mg protein, 100% D2O | 100% D2O
Resolution not provided
5O0U Crystal structure of tarantula venom peptide Protoxin-II Deposited 2017-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–30（30 aa）
Not recorded CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2M lithium sulfate, 100 mM Tris-HCl (pH 8), 2% v/v PEG 400
Resolution 0.99 Å R-free 0.140
6MK4 Solution NMR structure of spider toxin analogue [E17K]ProTx-II Deposited 2018-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–30（30 aa）
Mutation：E17K No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions 298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR measurement conditions 298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition 2 mg/mL [E17K]ProTx-II, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6N4Q CryoEM structure of Nav1.7 VSD2 (actived state) in complex with the gating modifier toxin ProTx2 Deposited 2018-11-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric
Chain E 1–30（30 aa）
Chain F 1–30（30 aa）
Chain G 1–30（30 aa）
Chain H 1–30（30 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；10 mM Tris pH 8.0, 100 mM NaCl, 0.06% FA3, 0.1 mg/ml POPC:POPE:POPG mixed at molar ratio 3:1:1
cryo-EM vitrification conditions Cryogen ETHANE；Apply 3 uL, blot 2.5s. Ted Pella 595 filter paper.
Resolution 3.60 Å
6N4R CryoEM structure of Nav1.7 VSD2 (deactived state) in complex with the gating modifier toxin ProTx2 Deposited 2018-11-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric
Chain E 1–30（30 aa）
Chain F 1–30（30 aa）
Chain G 1–30（30 aa）
Chain H 1–30（30 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；10 mM Tris pH 8.0, 100 mM NaCl, 0.06% FA3, 0.1 mg/ml POPC:POPE:POPG mixed at molar ratio 3:1:1
cryo-EM vitrification conditions Cryogen ETHANE；Apply 3 uL, blot 2.5s. Ted Pella 595 filter paper.
Resolution 4.20 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6n4i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6n4i
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6n4i
Deposition date deposition_date2018-11-19
Structure title titleStructural basis of Nav1.7 inhibition by a gating-modifier spider toxin
Keywords keywordssodium channel, toxin, gating-modifier, voltage-gated, METAL TRANSPORT; METAL TRANSPORT
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier37.40 Å
Radius of gyration Rg (electron density) rg_electron36.35 Å
Forward intensity I(0) i0185296000.00
Molecular weight molecular_weight122920.0 kDa
Excluded volume excluded_volume159030 ų
Envelope volume envelope_volume207700 ų
Hydration-shell volume shell_volume48578 ų
Envelope diameter envelope_diameter135.9 Å
Shell Rg shell_rg41.48 Å
Envelope Rg envelope_rg36.76 Å
Shape Rg shape_rg36.30 Å
Total Rg total_rg36.92 Å
Total atoms total_atoms8629
Residues n_residues1021
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax126.8 Å
Rg (real space) rg_real37.33 Å
Rg uncertainty (real space) rg_real_error1.28 Å
I(0) (real space) i0_real1.8530e+08
I(0) uncertainty (real space) i0_real_error3.4730e+06
Rg (reciprocal space) rg_reciprocal37.38 Å
I(0) (reciprocal space) i0_reciprocal185300000.0000
Solution quality estimate total_estimate0.8846
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary45.3 Å
Skewness Skewness skewness0.246
Kurtosis Kurtosis kurtosis-0.308
Angular range angular_range— – 0.2100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10470000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.947
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)