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- PDB-9yfv: RCK Gating Ring from Kch in the Intermediate conformation -

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Basic information

Entry
Database: PDB / ID: 9yfv
TitleRCK Gating Ring from Kch in the Intermediate conformation
ComponentsVoltage-gated potassium channel Kch
KeywordsTRANSPORT PROTEIN / Ion Channel Gating ring / RCK / Potassium Channel / MEMBRANE 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsMorote-Costas, B. / Zhou, M.
Funding support1items
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
DepositionSep 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Voltage-gated potassium channel Kch
D: Voltage-gated potassium channel Kch
A: Voltage-gated potassium channel Kch
C: Voltage-gated potassium channel Kch


Theoretical massNumber of molelcules
Total (without water)262,7334
Polymers262,7334
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Voltage-gated potassium channel Kch


Mass: 65683.312 Da / Num. of mol.: 4 / Mutation: M240L (Uniprot numbering)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: kch, b1250, JW1242 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31069
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1RCK Domain DimerCOMPLEXall0RECOMBINANT
2KCH Ion ChannelCOMPLEXall1RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.155320 MDaYES
210.019 MDaYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Escherichia coli (E. coli)83333K-12
32Escherichia coli (E. coli)83333K-12
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli BL21(DE3) (bacteria)469008
32Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMPotassium ChlorideKCl1
220 mMHEPESC8H18N2O4S1
3.1 %LMNGC47H88O221
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 281.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 800 nm / Nominal defocus min: 200 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.9particle selection
12cryoSPARC3.93D reconstruction
19PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 18170630
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 292104 / Symmetry type: POINT
Atomic model buildingPDB-ID: 1ID1

1id1


Accession code: 1ID1 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.92 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029148
ELECTRON MICROSCOPYf_angle_d0.48212394
ELECTRON MICROSCOPYf_dihedral_angle_d4.0381258
ELECTRON MICROSCOPYf_chiral_restr0.0421546
ELECTRON MICROSCOPYf_plane_restr0.0031628

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