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- EMDB-47930: Cryo-EM structure of the human KCa3.1/calmodulin channel in compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-47930
TitleCryo-EM structure of the human KCa3.1/calmodulin channel in complex with Ca2+ and 1,4-dihydropyridine (DHP-103)
Map dataSmall-conductance Ca2 -activated K channels bound to 1,4-dihydropyridine (DHP-103)
Sample
  • Complex: Human SK4-CaM channel complex in the presence of calcium.
    • Protein or peptide: Intermediate conductance calcium-activated potassium channel protein 4
    • Protein or peptide: Calmodulin-1
  • Ligand: POTASSIUM ION
  • Ligand: CALCIUM ION
KeywordsIon channel / Membrane protein / Ca-binding protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


intermediate conductance calcium-activated potassium channel activity / saliva secretion / small conductance calcium-activated potassium channel activity / stabilization of membrane potential / Ca2+ activated K+ channels / macropinocytosis / calcium-activated potassium channel activity / regulation of calcium ion import across plasma membrane / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding ...intermediate conductance calcium-activated potassium channel activity / saliva secretion / small conductance calcium-activated potassium channel activity / stabilization of membrane potential / Ca2+ activated K+ channels / macropinocytosis / calcium-activated potassium channel activity / regulation of calcium ion import across plasma membrane / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / positive regulation of potassium ion transmembrane transport / establishment of protein localization to membrane / cell volume homeostasis / phospholipid translocation / nitric-oxide synthase binding / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of synaptic vesicle exocytosis / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of T cell receptor signaling pathway / negative regulation of ryanodine-sensitive calcium-release channel activity / calcineurin-mediated signaling / regulation of synaptic vesicle endocytosis / protein phosphatase activator activity / postsynaptic cytosol / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / immune system process / catalytic complex / potassium channel activity / detection of calcium ion / regulation of cardiac muscle contraction / phosphatidylinositol 3-kinase binding / presynaptic cytosol / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / voltage-gated potassium channel complex / calcium channel regulator activity / potassium ion transmembrane transport / sperm midpiece / calcium channel complex / calyx of Held / nitric-oxide synthase regulator activity / response to amphetamine / adenylate cyclase activator activity / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / regulation of cytokinesis / positive regulation of protein secretion / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / establishment of localization in cell / defense response / potassium ion transport / Schaffer collateral - CA1 synapse / cellular response to type II interferon / ruffle membrane / response to calcium ion / spindle pole / calcium ion transport / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / myelin sheath / growth cone / protein phosphatase binding / protein homotetramerization / vesicle / transmembrane transporter binding / calmodulin binding / neuron projection / protein domain specific binding / neuronal cell body / centrosome / calcium ion binding / protein kinase binding / protein homodimerization activity / protein-containing complex / mitochondrion / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Calmodulin-binding domain / Potassium channel, calcium-activated, SK / SK, calmodulin-binding domain superfamily / Calmodulin binding domain / Calcium-activated SK potassium channel / Calmodulin binding domain / Potassium channel domain / Ion channel / : / EF-hand domain pair ...Calmodulin-binding domain / Potassium channel, calcium-activated, SK / SK, calmodulin-binding domain superfamily / Calmodulin binding domain / Calcium-activated SK potassium channel / Calmodulin binding domain / Potassium channel domain / Ion channel / : / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Intermediate conductance calcium-activated potassium channel protein 4 / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsNam YW / Zhang M
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)4R33 NS101182-03 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1R15 NS130420-01A1 United States
American Heart Association23AIREA1039423 United States
American Heart Association24CDA1260237 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Design and structural basis of selective 1,4-dihydropyridine inhibitors of the calcium-activated potassium channel K3.1.
Authors: Seow Theng Ong / Young-Woo Nam / Joshua A Nasburg / Alena Ramanishka / Xuan Rui Ng / Zhong Zhuang / Stephanie Shee Min Goay / Hai M Nguyen / Latika Singh / Vikrant Singh / Alicia Rivera / M ...Authors: Seow Theng Ong / Young-Woo Nam / Joshua A Nasburg / Alena Ramanishka / Xuan Rui Ng / Zhong Zhuang / Stephanie Shee Min Goay / Hai M Nguyen / Latika Singh / Vikrant Singh / Alicia Rivera / M Elaine Eyster / Yang Xu / Seth L Alper / Heike Wulff / Miao Zhang / K George Chandy /
Abstract: The 1,4-dihydropyridines, drugs with well-established bioavailability and toxicity profiles, have proven efficacy in treating human hypertension, peripheral vascular disorders, and coronary artery ...The 1,4-dihydropyridines, drugs with well-established bioavailability and toxicity profiles, have proven efficacy in treating human hypertension, peripheral vascular disorders, and coronary artery disease. Every 1,4-dihydropyridine in clinical use blocks L-type voltage-gated calcium channels. We now report our development, using selective optimization of a side activity (SOSA), of a class of 1,4-dihydropyridines that selectively and potently inhibit the intermediate-conductance calcium-activated K channel K3.1, a validated therapeutic target for diseases affecting many organ systems. One of these 1,4-dihydropyridines, DHP-103, blocked K3.1 with an IC of 6 nM and exhibited exquisite selectivity over calcium channels and a panel of >100 additional molecular targets. Using high-resolution structure determination by cryogenic electron microscopy together with mutagenesis and electrophysiology, we delineated the drug binding pocket for DHP-103 within the water-filled central cavity of the K3.1 channel pore, where bound drug directly impedes ion permeation. DHP-103 inhibited gain-of-function mutant K3.1 channels that cause hereditary xerocytosis, suggesting its potential use as a therapeutic for this hemolytic anemia. In a rat model of acute ischemic stroke, the second leading cause of death worldwide, DHP-103 administered 12 h postischemic insult in proof-of-concept studies reduced infarct volume, improved balance beam performance (measure of proprioception) and decreased numbers of activated microglia in infarcted areas. K3.1-selective 1,4-dihydropyridines hold promise for the many diseases for which K3.1 has been experimentally confirmed as a therapeutic target.
History
DepositionNov 15, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47930.png

Downloads & links

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Map

FileDownload / File: emd_47930.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSmall-conductance Ca2 -activated K channels bound to 1,4-dihydropyridine (DHP-103)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.86 Å/pix.
x 500 pix.
= 430. Å		0.86 Å/pix.
x 500 pix.
= 430. Å		0.86 Å/pix.
x 500 pix.
= 430. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0
Minimum - Maximum-58.407299999999999 - 71.732110000000006
Average (Standard dev.)0.000000000001141 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 430.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of Small-conductance Ca2 -activated K channels...

Fileemd_47930_half_map_1.map
AnnotationHalf map of Small-conductance Ca2 -activated K channels bound to 1,4-dihydropyridine (DHP-103)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of Small-conductance Ca2 -activated K channels...

Fileemd_47930_half_map_2.map
AnnotationHalf map of Small-conductance Ca2 -activated K channels bound to 1,4-dihydropyridine (DHP-103)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human SK4-CaM channel complex in the presence of calcium.

EntireName: Human SK4-CaM channel complex in the presence of calcium.
Components
  • Complex: Human SK4-CaM channel complex in the presence of calcium.
    • Protein or peptide: Intermediate conductance calcium-activated potassium channel protein 4
    • Protein or peptide: Calmodulin-1
  • Ligand: POTASSIUM ION
  • Ligand: CALCIUM ION

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Supramolecule #1: Human SK4-CaM channel complex in the presence of calcium.

SupramoleculeName: Human SK4-CaM channel complex in the presence of calcium.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 231.66 KDa

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Macromolecule #1: Intermediate conductance calcium-activated potassium channel protein 4

MacromoleculeName: Intermediate conductance calcium-activated potassium channel protein 4
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.598633 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LGALRRRKRL LEQEKSLAGW ALVLAGTGIG LMVLHAEMLW FGGCSWALYL FLVKCTISIS TFLLLCLIVA FHAKEVQLFM TDNGLRDWR VALTGRQAAQ IVLELVVCGL HPAPVRGPPC VQDLGAPLTS PQPWPGFLGQ GEALLSLAML LRLYLVPRAV L LRSGVLLN ...String:
LGALRRRKRL LEQEKSLAGW ALVLAGTGIG LMVLHAEMLW FGGCSWALYL FLVKCTISIS TFLLLCLIVA FHAKEVQLFM TDNGLRDWR VALTGRQAAQ IVLELVVCGL HPAPVRGPPC VQDLGAPLTS PQPWPGFLGQ GEALLSLAML LRLYLVPRAV L LRSGVLLN ASYRSIGALN QVRFRHWFVA KLYMNTHPGR LLLGLTLGLW LTTAWVLSVA ERQAVNATGH LSDTLWLIPI TF LTIGYGD VVPGTMWGKI VCLCTGVMGV CCTALLVAVV ARKLEFNKAE KHVHNFMMDI QYTKEMKESA ARVLQEAWMF YKH TRRKES HAARRHQRKL LAAINAFRQV RLKHRKLREQ VNSMVDISKM HMILYDLQQN LS

UniProtKB: Intermediate conductance calcium-activated potassium channel protein 4

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Macromolecule #2: Calmodulin-1

MacromoleculeName: Calmodulin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 16.406004 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QLTEEQIAEF KEAFSLFDKD GDGTITTKEL GTVMRSLGQN PTEAELQDMI NEVDADGNGT IDFPEFLTMM ARKMKDTDSE EEIREAFRV FDKDGNGYIS AAELRHVMTN LGEKLTDEEV DEMIREADID GDGQVNYEEF VQMMTA

UniProtKB: Calmodulin-1

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Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 5 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 12 / Formula: CA
Molecular weightTheoretical: 40.078 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

Concentration2 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.3 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6cnn

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 109449
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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