9iti

Nav1.7 with mutations that eliminate beta1 binding

Method: ELECTRON MICROSCOPY Dmax: 122.4 Å Quality: REASONABLE

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

Sodium channel protein type 9 subunit alpha

Homo sapiens

UniProt Q15858

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Monomer Protein × 1 其他Polymer 2 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–1988 Not recorded 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 2 NA SODIUM ION × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 10 1PW (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 Y01 CHOLESTEROL HEMISUCCINATE × 4 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.92 Å

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.

42 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SCN9A_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 44–2030; UniProt 1–1988

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 9iti

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9iti
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9iti
Deposition date deposition_date2024-07-20
最后修订 last_revision2025-08-20
Structure title titleNav1.7 with mutations that eliminate beta1 binding
Keywords keywordsVoltage-gated sodium channel, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier38.30
Radius of gyration Rg (electron density) rg_electron37.29
Forward intensity I(0) i0290717000.00
Molecular weight molecular_weight157620.0 kDa
Excluded volume excluded_volume205470 ų
Envelope volume envelope_volume276590 ų
Hydration-shell volume shell_volume60739 ų
Envelope diameter envelope_diameter126.5
Shell Rg shell_rg44.05
Envelope Rg envelope_rg37.60
Shape Rg shape_rg37.32
Total Rg total_rg37.67
Total atoms total_atoms11072
Residues n_residues1268
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax122.4
Rg (real space) rg_real38.12
Rg uncertainty (real space) rg_real_error0.80
I(0) (real space) i0_real2.9070e+08
I(0) uncertainty (real space) i0_real_error4.6130e+06
Rg (reciprocal space) rg_reciprocal38.23
I(0) (reciprocal space) i0_reciprocal290700000.0000
Solution quality estimate total_estimate0.6652
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary50.8
Skewness Skewness skewness0.195
Kurtosis Kurtosis kurtosis-0.372
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha27330000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 0.035; Positv: 1.000; Valcen: 0.987; Smooth: 0.879

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (10)

8. Citations (1)

9. Files and Curves (10)