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- EMDB-73056: RCK Gating Ring from Kch in the open conformation in the presence... -

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Basic information

Entry
Database: EMDB / ID: EMD-73056
TitleRCK Gating Ring from Kch in the open conformation in the presence of zinc
Map data
Sample
  • Complex: RCK Domain Dimer
    • Protein or peptide: Voltage-gated potassium channel Kch
    • Protein or peptide: Voltage-gated potassium channel Kch
KeywordsIon Channel Gating ring / RCK / Potassium Channel / MEMBRANE PROTEIN / TRANSPORT PROTEIN
Function / homology
Function and homology information


potassium channel activity / potassium ion transport / potassium ion transmembrane transport / protein-containing complex / identical protein binding / plasma membrane
Similarity search - Function
: / TrkA-N domain / 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
Voltage-gated potassium channel Kch
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsMorote-Costas B / Zhou M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: PNAS Nexus / Year: 2026
Title: Mechanism of Kch activation by Zn.
Authors: Brian Morote-Costas / Yaping Pan / Lie Wang / Xiaochen Bai / Steve W Lockless / Ming Zhou /
Abstract: has a single K channel gene, , that produces a K channel with six transmembrane segments and a cytosolic Regulate Conductance of K channels (RCK) domain. RCK domains are present in both eukaryotic ... has a single K channel gene, , that produces a K channel with six transmembrane segments and a cytosolic Regulate Conductance of K channels (RCK) domain. RCK domains are present in both eukaryotic and prokaryotic organisms and known to regulate ion channel activity upon binding of an ion or a nucleotide, however, how Kch is regulated remains unknown. Here, we show that Zn or Cu activates Kch via the RCK domain. Structural studies reveal that eight RCK domains assemble into a gating ring that can assume three conformations, closed, intermediate, and open, and that Zn promotes the open conformation by stabilizing the assembly interface. These results expand our knowledge on Kch and on RCK-mediated regulation of ion channels.
History
DepositionOct 7, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73056.png

Downloads & links

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Map

FileDownload / File: emd_73056.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.992 Å		0.83 Å/pix.
x 256 pix.
= 212.992 Å		0.83 Å/pix.
x 256 pix.
= 212.992 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.8241627 - 3.0698266
Average (Standard dev.)0.0051494865 (±0.08993831)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.992 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73056_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_73056_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73056_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : RCK Domain Dimer

EntireName: RCK Domain Dimer
Components
  • Complex: RCK Domain Dimer
    • Protein or peptide: Voltage-gated potassium channel Kch
    • Protein or peptide: Voltage-gated potassium channel Kch

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Supramolecule #1: RCK Domain Dimer

SupramoleculeName: RCK Domain Dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K-12
Molecular weightTheoretical: 261.914 MDa

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Macromolecule #1: Voltage-gated potassium channel Kch

MacromoleculeName: Voltage-gated potassium channel Kch / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K-12
Molecular weightTheoretical: 46.105371 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSHWATFKQT ATNLWVTLRH DILALAVFLN GLLIFKTIYG MSVNLLDIFH IKAFSELDLS LLANAPLFML GVFLVLNSIG LLFRAKLAW AISIILLLIA LIYTLHFYPW LKFSIGFCIF TLVFLLILRK DFSHSSAAAG TIFAFISFTT LLFYSTYGAL Y LSEGFNPR ...String:
MSHWATFKQT ATNLWVTLRH DILALAVFLN GLLIFKTIYG MSVNLLDIFH IKAFSELDLS LLANAPLFML GVFLVLNSIG LLFRAKLAW AISIILLLIA LIYTLHFYPW LKFSIGFCIF TLVFLLILRK DFSHSSAAAG TIFAFISFTT LLFYSTYGAL Y LSEGFNPR IESLMTAFYF SIETMSTVGY GDIVPVSESA RLFTISVIIS GITVFATSMT SIFGPLIRGG FNKLVKGNNH TM HRKDHFI VCGHSILAIN TILQLNQRGQ NVTVISNLPE DDIKQLEQRL GDNADVIPGD SNDSSVLKKA GIDRCRAILA LSD NDADNA FVVLSAKDMS SDVKTVLAVS DSKNLNKIKM VHPDIILSPQ LFGSEILARV LNGEEINNDM LVSMLLNSGH GIFS DNDEL ETKADSKESA QK

UniProtKB: Voltage-gated potassium channel Kch

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Macromolecule #2: Voltage-gated potassium channel Kch

MacromoleculeName: Voltage-gated potassium channel Kch / type: protein_or_peptide / ID: 2
Details: shorter isoform, beginning with alternate start codon at M240
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K-12
Molecular weightTheoretical: 19.456959 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MHRKDHFIVC GHSILAINTI LQLNQRGQNV TVISNLPEDD IKQLEQRLGD NADVIPGDSN DSSVLKKAGI DRCRAILALS DNDADNAFV VLSAKDMSSD VKTVLAVSDS KNLNKIKMVH PDIILSPQLF GSEILARVLN GEEINNDMLV SMLLNSGHGI F SDNDELET KADSKESAQK

UniProtKB: Voltage-gated potassium channel Kch

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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: 7.4
Component:
ConcentrationFormulaName
150.0 mMKClPotassium Chloride
20.0 mMC8H18N2O4SHEPES
0.1 %C47H88O22LMNG
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV

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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: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.8 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 81000
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

Particle selectionNumber selected: 18170630
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1id1

Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.9) / Number images used: 185079
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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