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- PDB-7yo1: Cryo-EM structure of RCK1 mutated human Slo1-LRRC26 complex -

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Basic information

Entry
Database: PDB / ID: 7yo1
TitleCryo-EM structure of RCK1 mutated human Slo1-LRRC26 complex
Components
  • Calcium-activated potassium channel subunit alpha-1
  • Leucine-rich repeat-containing protein 26
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


positive regulation of voltage-gated potassium channel activity / monoatomic ion-gated channel activity / potassium channel activator activity / ligand-gated monoatomic cation channel activity / voltage-gated potassium channel activity / potassium channel activity / potassium channel regulator activity / voltage-gated potassium channel complex / potassium ion transmembrane transport / transmembrane transporter binding ...positive regulation of voltage-gated potassium channel activity / monoatomic ion-gated channel activity / potassium channel activator activity / ligand-gated monoatomic cation channel activity / voltage-gated potassium channel activity / potassium channel activity / potassium channel regulator activity / voltage-gated potassium channel complex / potassium ion transmembrane transport / transmembrane transporter binding / cytoskeleton / extracellular exosome / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / : / Ca2+-activated K+ channel Slowpoke, TrkA_C like domain / Calcium-activated potassium channel BK, alpha subunit / : / Calcium-activated BK potassium channel alpha subunit / Calcium-activated potassium channel slowpoke-like RCK domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...: / : / Ca2+-activated K+ channel Slowpoke, TrkA_C like domain / Calcium-activated potassium channel BK, alpha subunit / : / Calcium-activated BK potassium channel alpha subunit / Calcium-activated potassium channel slowpoke-like RCK domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Ion transport domain / Ion transport protein / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Calcium-activated potassium channel subunit alpha-1 / Leucine-rich repeat-containing protein 26
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsYamanouchi, D. / Nureki, O.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Structural basis for dual allosteric gating modulation of Slo1-LRRC channel complex
Authors: Yamanouchi, D.
History
DepositionAug 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calcium-activated potassium channel subunit alpha-1
B: Leucine-rich repeat-containing protein 26
C: Calcium-activated potassium channel subunit alpha-1
D: Leucine-rich repeat-containing protein 26
E: Calcium-activated potassium channel subunit alpha-1
F: Leucine-rich repeat-containing protein 26
G: Calcium-activated potassium channel subunit alpha-1
H: Leucine-rich repeat-containing protein 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)617,47420
Polymers617,0568
Non-polymers41812
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Calcium-activated potassium channel subunit alpha-1 / Calcium-activated potassium channel / subfamily M subunit alpha-1 / K(VCA)alpha / KCa1.1


Mass: 119370.484 Da / Num. of mol.: 4 / Mutation: D372A, D367A, K577S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNMA1 / Cell line (production host): HEK293S GnTl- / Production host: Homo sapiens (human) / References: UniProt: A0A1W2PRB0
#2: Protein
Leucine-rich repeat-containing protein 26 / BK channel auxiliary gamma subunit LRRC26 / Cytokeratin-associated protein in cancer


Mass: 34893.629 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRRC26, CAPC / Cell line (production host): HEK293S GnTl- / Production host: Homo sapiens (human) / References: UniProt: Q2I0M4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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

ComponentName: human Slo1-LRRC26 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 616 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293S GnTl-
Buffer solutionpH: 8
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48940 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00336590
ELECTRON MICROSCOPYf_angle_d0.52449734
ELECTRON MICROSCOPYf_dihedral_angle_d3.2714908
ELECTRON MICROSCOPYf_chiral_restr0.0385739
ELECTRON MICROSCOPYf_plane_restr0.0046278

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