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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 / potassium ion transport / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Scorpion short toxins signature. / Scorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / : / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / TrkA-N domain / Knottin, scorpion toxin-like superfamily ...Scorpion short toxins signature. / Scorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / : / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / TrkA-N domain / Knottin, scorpion toxin-like superfamily / Regulator of K+ conductance, N-terminal / RCK N-terminal domain profile. / 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: Denis Qoraj / Swantje Mohr / Yessenbek K Aldakul / Thiemo Sprink / Carl Öster / Taoran Xiao / Peter Schmieder / Sascha Lange / Tillmann Utesch / Daniel Roderer / Shanshuang Chen / Han Sun / Adam Lange /
Abstract: Scorpion toxins block potassium channels, disrupting cellular excitability and causing symptoms such as pain, muscle spasms, or paralysis. Here, we use an integrated structural biology approach to ...Scorpion toxins block potassium channels, disrupting cellular excitability and causing symptoms such as pain, muscle spasms, or paralysis. Here, we use an integrated structural biology approach to uncover the binding mode of the scorpion toxin charybdotoxin (CTX) to the MthK channel, a model system for human large-conductance potassium (BK) channels. Cryo-EM defines the overall architecture of the MthK-CTX complex, while complementary solution- and solid-state NMR experiments identify key binding residues and show that toxin engagement alters the selectivity filter (SF) ion configuration without rearranging the filter itself. NMR and MD simulations further reveal an anchoring lysine residue stably inserted into the SF, while other contacts undergo fast NMR timescale dynamics. Together, these findings explain how CTX-like toxins maintain exceptionally high affinity while tolerating binding across multiple K⁺ channel subtypes, paving the way for site-specific extracellular modulation.
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
Revision 1.1Sep 2, 2026Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.page_first / _citation.pdbx_database_id_PubMed ..._citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.1Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.page_first / _citation.pdbx_database_id_PubMed ..._citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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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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