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2mi5

Structure of insect-specific sodium channel toxin mu-Dc1a

Method: SOLUTION NMR Dmax: 41.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Mu-diguetoxin-Dc1a

Diguetia canities

UniProt P49126

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 39–94 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 5；298 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient NMR sample composition：350 uM [U-99% 13C; U-99% 15N] Dc1a-1, 20 mM sodium acetate-2, 95% H2O/5% D2O | 95% H2O/5% D2O Resolution not provided

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 2MI5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6A90 Complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana and Dc1a Deposited 2018-07-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 39–94（56 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6A91 Complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana bound with saxitoxin and Dc1a Deposited 2018-07-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 39–94（56 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 9SL [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6A95 Complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana bound with tetrodotoxin and Dc1a Deposited 2018-07-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 39–94（56 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 9SR (1R,5R,6R,7R,9S,11S,12S,13S,14S)-3-amino-14-(hydroxymethyl)-8,10-dioxa-2,4-diazatetracyclo[7.3.1.1~7,11~.0~1,6~]tetradec-3-ene-5,9,12,13,14-pentol (non-preferred name) × 1 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8F0S Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the hybrid inhibitor GNE-9296 Deposited 2022-11-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 39–94（56 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X80 5-chloro-4-(cyclopentylmethoxy)-N-(4-{[(1S,2S)-2-(dimethylamino)cyclohexyl]amino}-2-fluorobenzene-1-sulfonyl)-2-fluorobenzamide × 1 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 1 Y01 CHOLESTEROL HEMISUCCINATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TXI92_DIGCA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–57； UniProt 39–94

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 2mi5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2mi5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2mi5
Deposition date deposition_date2013-12-08
Structure title titleStructure of insect-specific sodium channel toxin mu-Dc1a
Keywords keywords;spider venom, insecticidal toxin, sodium channel, voltage-sensor, gating modifier, non-uniform sampling, DTX9.2, toxin, inhibitor cystine knot, knottin ;; TOXIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier11.58 Å
Radius of gyration Rg (electron density) rg_electron12.16 Å
Forward intensity I(0) i0268372000.00
Molecular weight molecular_weight129530.0 kDa
Excluded volume excluded_volume158230 ų
Envelope volume envelope_volume14260 ų
Hydration-shell volume shell_volume9506 ų
Envelope diameter envelope_diameter49.1 Å
Shell Rg shell_rg18.53 Å
Envelope Rg envelope_rg14.10 Å
Shape Rg shape_rg12.22 Å
Total Rg total_rg12.11 Å
Total atoms total_atoms17340
Residues n_residues1140
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 dmax41.1 Å
Rg (real space) rg_real11.63 Å
Rg uncertainty (real space) rg_real_error0.36 Å
I(0) (real space) i0_real2.6840e+08
I(0) uncertainty (real space) i0_real_error2.5910e+06
Rg (reciprocal space) rg_reciprocal11.63 Å
I(0) (reciprocal space) i0_reciprocal268400000.0000
Solution quality estimate total_estimate0.7674
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary12.5 Å
Skewness Skewness skewness0.423
Kurtosis Kurtosis kurtosis-0.299
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha78700.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.727; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.794; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2mi5A00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology130 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4
Homologous superfamily homologous superfamily120 —
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8. Citations (3)

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9. Files and Curves (10)