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- PDB-28no: CTX/MthK complex -

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Basic information

Entry
Database: PDB / ID: 28no
TitleCTX/MthK complex
Components
  • Calcium-gated potassium channel MthK
  • Potassium channel toxin alpha-KTx 1.1
KeywordsMEMBRANE PROTEIN / Toxin-Ion channel complex
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / ion channel inhibitor activity / defense response to fungus / potassium channel regulator activity / potassium ion transport / toxin activity / killing of cells of another organism / defense response to bacterium / extracellular region / metal ion binding ...monoatomic cation transmembrane transporter activity / ion channel inhibitor activity / defense response to fungus / potassium channel regulator activity / potassium ion transport / toxin activity / killing of cells of another organism / defense response to bacterium / extracellular region / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Scorpion short toxins signature. / Scorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / : / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Regulator of K+ conductance, N-terminal ...Scorpion short toxins signature. / Scorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / : / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Regulator of K+ conductance, N-terminal / RCK N-terminal domain profile. / Knottin, scorpion toxin-like superfamily / Potassium channel domain / Ion channel / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / Calcium-gated potassium channel MthK / Potassium channel toxin alpha-KTx 1.1
Similarity search - Component
Biological speciesLeiurus hebraeus (scorpion)
Methanothermobacter thermautotrophicus str. Delta H (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsQoraj, D. / Sprink, T. / Lange, A.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2008/1 UniSysCat 390540038 Germany
Leibniz AssociationK305/2020 Germany
CitationJournal: Nat Commun / Year: 2026
Title: Atomic structure and plasticity of the CTX-MthK complex investigated by cryo-EM, NMR, and MD simulations
Authors: Qoraj, D. / Mohr, S. / Aldakul, Y.K. / Sprink, T. / Oster, C. / Xiao, T. / Schmieder, P. / Lange, S. / Utesch, T. / Roderer, D. / Chen, S. / Sun, H. / Lange, A.
History
DepositionFeb 10, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Potassium channel toxin alpha-KTx 1.1
A: Calcium-gated potassium channel MthK
B: Calcium-gated potassium channel MthK
C: Calcium-gated potassium channel MthK
D: Calcium-gated potassium channel MthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,9226
Polymers157,8835
Non-polymers391
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide Potassium channel toxin alpha-KTx 1.1 / ChTX-Lq1 / ChTx-a / Charybdotoxin / CTX / ChTX


Mass: 4309.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The N-terminal glutamine (or glutamate) residues is cyclized to a pyroglutamte.
Source: (gene. exp.) Leiurus hebraeus (scorpion) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): K12 HMS174 / References: UniProt: P13487
#2: Protein
Calcium-gated potassium channel MthK


Mass: 38393.277 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Truncated version of MthK
Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea)
Strain: DeltaH / Gene: mthK, MTH_1520 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: O27564
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1CTX/MthK complexCOMPLEX#1-#20RECOMBINANT
2Charybdotoxin (CTX)ORGANELLE OR CELLULAR COMPONENT#11RECOMBINANT
3MthKORGANELLE OR CELLULAR COMPONENT#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
11307.7 kDa/nmNO
214.31 kDa/nmNO
31303.39 kDa/nmNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Methanothermobacter thermautotrophicus str. Delta H (archaea)187420
32Leiurus hebraeus (scorpion)2899558
43Methanothermobacter thermautotrophicus str. Delta H (archaea)187420
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainPlasmid
21Escherichia coli (E. coli)562XL1-bluepQE60
32Escherichia coli (E. coli)562K12 HMS174pET28a
43Escherichia coli (E. coli)562XL1-bluepQE60
Buffer solutionpH: 7.6 / Details: 20 mM HEPES, pH 7.6, 100 mM KCl
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2100 mMPotassium chlorideKCl1
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.86 sec. / Electron dose: 60.76 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
2PHENIX1.21.2_5419model refinement
5RELION5CTF correction
10RELION5initial Euler assignment
11RELION5final Euler assignment
12RELION5classification
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92302 / Num. of class averages: 1 / Symmetry type: POINT
RefinementHighest resolution: 4.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033156
ELECTRON MICROSCOPYf_angle_d0.6224296
ELECTRON MICROSCOPYf_dihedral_angle_d12.5551073
ELECTRON MICROSCOPYf_chiral_restr0.039519
ELECTRON MICROSCOPYf_plane_restr0.007509

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