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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 / 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 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: Qoraj D / Mohr S / Aldakul YK / Sprink T / Oster C / Xiao T / Schmieder P / Lange S / Utesch T / Roderer D / Chen S / Sun H / Lange A
History
DepositionFeb 10, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 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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