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- PDB-9zs7: CryoEM structure of Shaker ILT (V369I,I372L,S376T) -

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Basic information

Entry
Database: PDB / ID: 9zs7
TitleCryoEM structure of Shaker ILT (V369I,I372L,S376T)
ComponentsPotassium voltage-gated channel protein Shaker
KeywordsMEMBRANE PROTEIN / potassium ion channel / Triple mutation / Intermediate VSD / Closed state pore
Function / homology
Function and homology information


mating behavior, sex discrimination / Phase 3 - rapid repolarisation / behavioral response to ether / Voltage gated Potassium channels / proboscis extension reflex / larval locomotory behavior / regulation of synaptic activity / courtship behavior / positive regulation of membrane potential / regulation of circadian sleep/wake cycle, sleep ...mating behavior, sex discrimination / Phase 3 - rapid repolarisation / behavioral response to ether / Voltage gated Potassium channels / proboscis extension reflex / larval locomotory behavior / regulation of synaptic activity / courtship behavior / positive regulation of membrane potential / regulation of circadian sleep/wake cycle, sleep / axon extension / positive regulation of circadian sleep/wake cycle, sleep / detection of visible light / delayed rectifier potassium channel activity / cellular response to dopamine / sleep / voltage-gated monoatomic cation channel activity / sensory perception of taste / action potential / potassium ion transport / voltage-gated potassium channel activity / voltage-gated potassium channel complex / potassium ion transmembrane transport / protein homooligomerization / perikaryon / learning or memory / neuron projection / membrane raft / membrane
Similarity search - Function
Potassium channel, voltage dependent, Kv1 / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Voltage-gated potassium channel / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily / SKP1/BTB/POZ domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
: / Potassium voltage-gated channel protein Shaker
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsAgrawal, R. / Perozo, E. / Roux, B.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director5R35GM152124 United States
National Institutes of Health/Office of the Director5R01GM150272 United States
National Institutes of Health/Office of the Director1S10OD028655 United States
CitationJournal: To Be Published
Title: CryoEM structure of Shaker ILT mutant
Authors: Agrawal, R. / Perozo, E. / Roux, B.
History
DepositionDec 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium voltage-gated channel protein Shaker
B: Potassium voltage-gated channel protein Shaker
D: Potassium voltage-gated channel protein Shaker
C: Potassium voltage-gated channel protein Shaker
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,3829
Polymers297,1874
Non-polymers1955
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 107 - 491 / Label seq-ID: 107 - 491

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CD
d_4DC

NCS oper:
IDCodeMatrixVector
1given(-0.00115246711974, 0.999999326159, 0.000139643676394), (-0.999997666752, -0.00115221004093, -0.00182726660392), (-0.00182710447379, -0.000141749215251, 0.999998320797)0.205981146122, 299.477229067, 0.313503767823
2given(0.00114502915446, -0.999999326423, 0.000189899593027), (0.999998294967, 0.00114530305567, 0.00144856589641), (-0.00144878241327, 0.000188240619059, 0.999998932797)298.782279829, -0.377365794713, 0.21034436491
3given(-0.999998462336, -0.00111512824002, -0.00135344512602), (0.00111488120804, -0.999999361727, 0.000183261615194), (-0.00135364862235, 0.000181752402862, 0.9999990673)299.397300054, 298.785658145, 0.18614836462

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Components

#1: Protein
Potassium voltage-gated channel protein Shaker / Protein minisleep


Mass: 74296.727 Da / Num. of mol.: 4 / Mutation: V369I, I372L, S376T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Sh, mns, CG12348 / Production host: Homo sapiens (human) / References: UniProt: P08510
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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

ComponentName: Potassium ion channel with 6 transmembrane helices and T1 domain
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.069 MDa / Experimental value: NO
Source (natural)Organism: Drosophila melanogaster (Fruit fly) (fruit fly)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5 / Details: 150mM KCl, 50mM Tris-Cl, 0.02% GDN
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 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: OTHER
Electron lensMode: OTHER / Nominal magnification: 81000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 700 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 6.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 6600

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
7Cootmodel fitting
8ISOLDEmodel fitting
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
14PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 293000 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE
Atomic model buildingPDB-ID: 7SIP

7sip


Accession code: 7SIP / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 47.69 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002110452
ELECTRON MICROSCOPYf_angle_d0.470414288
ELECTRON MICROSCOPYf_chiral_restr0.03551744
ELECTRON MICROSCOPYf_plane_restr0.00411792
ELECTRON MICROSCOPYf_dihedral_angle_d10.13343532
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints4.02777005439E-11
ens_1d_3AAELECTRON MICROSCOPYNCS constraints1.28737439406E-12
ens_1d_4AAELECTRON MICROSCOPYNCS constraints5.89688029142E-13

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