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- EMDB-56657: CTX/MthK complex -

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Basic information

Entry
Database: EMDB / ID: EMD-56657
TitleCTX/MthK complex
Map dataPost-processed C1 reconstruction of the CTX/MthK complex.
Sample
  • Complex: CTX/MthK complex
    • Organelle or cellular component: Charybdotoxin (CTX)
      • Protein or peptide: Potassium channel toxin alpha-KTx 1.1
    • Organelle or cellular component: MthK
      • Protein or peptide: Calcium-gated potassium channel MthK
  • Ligand: POTASSIUM ION
KeywordsToxin-Ion channel complex / MEMBRANE PROTEIN
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 speciesMethanothermobacter thermautotrophicus str. Delta H (archaea) / Leiurus hebraeus (scorpion)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsQoraj D / Sprink T / Lange A
Funding support Germany, 2 items
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, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56657.png

Downloads & links

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Map

FileDownload / File: emd_56657.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed C1 reconstruction of the CTX/MthK complex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0058
Minimum - Maximum-0.033047725 - 0.045210715
Average (Standard dev.)0.000024506942 (±0.00068163645)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-Map of the CTX/MthK reconstruction.

Fileemd_56657_half_map_1.map
AnnotationHalf-Map of the CTX/MthK reconstruction.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-Map of the CTX/MthK reconstruction.

Fileemd_56657_half_map_2.map
AnnotationHalf-Map of the CTX/MthK reconstruction.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CTX/MthK complex

EntireName: CTX/MthK complex
Components
  • Complex: CTX/MthK complex
    • Organelle or cellular component: Charybdotoxin (CTX)
      • Protein or peptide: Potassium channel toxin alpha-KTx 1.1
    • Organelle or cellular component: MthK
      • Protein or peptide: Calcium-gated potassium channel MthK
  • Ligand: POTASSIUM ION

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Supramolecule #1: CTX/MthK complex

SupramoleculeName: CTX/MthK complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Methanothermobacter thermautotrophicus str. Delta H (archaea)
Molecular weightTheoretical: 303.39 kDa/nm

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Supramolecule #2: Charybdotoxin (CTX)

SupramoleculeName: Charybdotoxin (CTX) / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Leiurus hebraeus (scorpion)

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Supramolecule #3: MthK

SupramoleculeName: MthK / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Methanothermobacter thermautotrophicus str. Delta H (archaea)

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Macromolecule #1: Potassium channel toxin alpha-KTx 1.1

MacromoleculeName: Potassium channel toxin alpha-KTx 1.1 / type: protein_or_peptide / ID: 1
Details: The N-terminal glutamine (or glutamate) residues is cyclized to a pyroglutamte.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Leiurus hebraeus (scorpion)
Molecular weightTheoretical: 4.309998 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(PCA)FTNVSCTTS KECWSVCQRL HNTSRGKCMN KKCRCYS

UniProtKB: Potassium channel toxin alpha-KTx 1.1

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Macromolecule #2: Calcium-gated potassium channel MthK

MacromoleculeName: Calcium-gated potassium channel MthK / type: protein_or_peptide / ID: 2 / Details: Truncated version of MthK / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Methanothermobacter thermautotrophicus str. Delta H (archaea)
Strain: DeltaH
Molecular weightTheoretical: 38.393277 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVLVIEIIRK HLPRVLKVPA TRILLLVLAV IIYGTAGFHF IEGESWTVSL YWTFVTIATV GYGDYSPSTP LGMYFTVTLI VLGIGTFAV AVERLLEFLI NREQMKLMGL IDVAKSRHVV ICGWSESTLE CLRELRGSEV FVLAEDENVR KKVLRSGANF V HGDPTRVS ...String:
MVLVIEIIRK HLPRVLKVPA TRILLLVLAV IIYGTAGFHF IEGESWTVSL YWTFVTIATV GYGDYSPSTP LGMYFTVTLI VLGIGTFAV AVERLLEFLI NREQMKLMGL IDVAKSRHVV ICGWSESTLE CLRELRGSEV FVLAEDENVR KKVLRSGANF V HGDPTRVS DLEKANVRGA RAVIVDLESD SETIHCILGI RKIDESVRII AEAERYENIE QLRMAGADQV ISPFVISGRL MS RSIDDGY EAMFVQDVLA EESTRRMVEV PIPEGSKLEG VSVLDADIHD VTGVIIIGVG RGDELIIDPP RDYSFRAGDI ILG IGKPEE IERLKNYISA LEENLYFQ

UniProtKB: Calcium-gated potassium channel MthK

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Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration8 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
100.0 mMKClPotassium chloride

Details: 20 mM HEPES, pH 7.6, 100 mM KCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 0.86 sec. / Average electron dose: 60.76 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 5.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 92302
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 106517 / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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