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- EMDB-48088: Cryo-EM structure of the mutant KCa2.2_F244S channel -

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Basic information

Entry
Database: EMDB / ID: EMD-48088
TitleCryo-EM structure of the mutant KCa2.2_F244S channel
Map dataEM map of mutant KCa2.2_F244S, missing S3-S4 loop.
Sample
  • Complex: Rat mutant KCa2.2_F244S channel complex with calmodulin in the presence of calcium
    • Protein or peptide: Small conductance calcium-activated potassium channel protein 2
    • Protein or peptide: Calmodulin-1
  • Ligand: POTASSIUM ION
  • Ligand: CALCIUM ION
  • Ligand: water
KeywordsIon channel / Calmodulin binding protein. Membrane protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


Ca2+ activated K+ channels / small conductance calcium-activated potassium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / calcium-activated potassium channel activity / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / positive regulation of potassium ion transport / inward rectifier potassium channel activity / establishment of protein localization to membrane / regulation of potassium ion transmembrane transport ...Ca2+ activated K+ channels / small conductance calcium-activated potassium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / calcium-activated potassium channel activity / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / positive regulation of potassium ion transport / inward rectifier potassium channel activity / establishment of protein localization to membrane / regulation of potassium ion transmembrane transport / nitric-oxide synthase binding / organelle localization by membrane tethering / regulation of synaptic vesicle exocytosis / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / presynaptic endocytosis / regulation of cardiac muscle cell action potential / negative regulation of ryanodine-sensitive calcium-release channel activity / alpha-actinin binding / regulation of synaptic vesicle endocytosis / regulation of neuronal synaptic plasticity / postsynaptic cytosol / protein phosphatase activator activity / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / catalytic complex / calcium channel regulator activity / detection of calcium ion / regulation of cardiac muscle contraction / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / smooth endoplasmic reticulum / presynaptic cytosol / cellular response to interferon-beta / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / voltage-gated potassium channel complex / T-tubule / sperm midpiece / potassium ion transmembrane transport / calcium channel complex / calyx of Held / nitric-oxide synthase regulator activity / response to amphetamine / adenylate cyclase activator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / regulation of cytokinesis / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / modulation of chemical synaptic transmission / potassium ion transport / sarcolemma / Schaffer collateral - CA1 synapse / cellular response to type II interferon / Z disc / spindle pole / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / myelin sheath / growth cone / postsynaptic membrane / dendritic spine / transmembrane transporter binding / calmodulin binding / protein domain specific binding / neuronal cell body / centrosome / calcium ion binding / protein kinase binding / glutamatergic synapse / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / nucleoplasm / membrane / 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
Calmodulin-1 / Small conductance calcium-activated potassium channel protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsNam YW / Zhang M
Funding support United States, 2 items
OrganizationGrant numberCountry
American Heart Association23AIREA1039423 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS101182-03 United States
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM structures of the small-conductance Ca2+-activated KCa2.2 channel
Authors: Nam YW / Im D / Santa Cruz Garcia A / Tringides ML / Nguyen HM / Liu Y / Orfali R / Ramanishka A / Pintilie G / Su CC / Cui M / Logothetis DE / Yu EW / Wulff H / Chandy KG / Zhang M
History
DepositionNov 26, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48088.png

Downloads & links

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Map

FileDownload / File: emd_48088.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of mutant KCa2.2_F244S, missing S3-S4 loop.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.86 Å/pix.
x 512 pix.
= 440.32 Å		0.86 Å/pix.
x 512 pix.
= 440.32 Å		0.86 Å/pix.
x 512 pix.
= 440.32 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: 6.5
Minimum - Maximum-90.829920000000001 - 102.681790000000007
Average (Standard dev.)-0.000000000002743 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 440.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: EM half map of mutant KCa2.2 F244S, missing S3-S4 loop.

Fileemd_48088_half_map_1.map
AnnotationEM half map of mutant KCa2.2_F244S, missing S3-S4 loop.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM half map of mutant KCa2.2 F244S, missing S3-S4 loop.

Fileemd_48088_half_map_2.map
AnnotationEM half map of mutant KCa2.2_F244S, missing S3-S4 loop.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rat mutant KCa2.2_F244S channel complex with calmodulin in the pr...

EntireName: Rat mutant KCa2.2_F244S channel complex with calmodulin in the presence of calcium
Components
  • Complex: Rat mutant KCa2.2_F244S channel complex with calmodulin in the presence of calcium
    • Protein or peptide: Small conductance calcium-activated potassium channel protein 2
    • Protein or peptide: Calmodulin-1
  • Ligand: POTASSIUM ION
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: Rat mutant KCa2.2_F244S channel complex with calmodulin in the pr...

SupramoleculeName: Rat mutant KCa2.2_F244S channel complex with calmodulin in the presence of calcium
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Mutant KCa2.2_F244S
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 230 KDa

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Macromolecule #1: Small conductance calcium-activated potassium channel protein 2

MacromoleculeName: Small conductance calcium-activated potassium channel protein 2
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 41.114754 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IGYKLGHRRA LFEKRKRLSD YALIFGMFGI VVMVIETELS WGAYDKASLY SLALKCLISL STIILLGLII VYHAREIQLF MVDNGADDW RIAMTYERIF FICLEILVCA IHPIPGNYTF TWTARLAFSY APSTTTADVD IILSIPMFLR LYLIARVMLL H SKLFTDAS ...String:
IGYKLGHRRA LFEKRKRLSD YALIFGMFGI VVMVIETELS WGAYDKASLY SLALKCLISL STIILLGLII VYHAREIQLF MVDNGADDW RIAMTYERIF FICLEILVCA IHPIPGNYTF TWTARLAFSY APSTTTADVD IILSIPMFLR LYLIARVMLL H SKLFTDAS SRSIGALNKI NFNTRFVMKT LMTICPGTVL LVFSISLWII AAWTVRACER YHDQQDVTSN FLGAMWLISI TF LSIGYGD MVPNTYCGKG VCLLTGIMGA GCTALVVAVV ARKLELTKAE KHVHNFMMDT QLTKRVKNAA ANVLRETWLI YKN TKLVKK IDHAKVRKHQ RKFLQAIHQL RSVKMEQRKL NDQAN

UniProtKB: Small conductance calcium-activated potassium channel protein 2

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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: 16.102626 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QLTEEQIAEF KEAFSLFDKD GDGTITTKEL GTVMRSLGQN PTEAELQDMI NEVDADGNGT IDFPEFLTMM ARKMKDTDSE EEIREAFRV FDKDGNGYIS AAELRHVMTN LGEKLTDEEV DEMIREADID GDGQVNYEEF VQM

UniProtKB: Calmodulin-1

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Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 4 / 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: 8 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration3 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

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8v2g

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81168
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

SoftwareName: UCSF ChimeraX (ver. 1.8)
Output model

PDB-9eio:
Cryo-EM structure of the mutant KCa2.2_F244S channel

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