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- EMDB-74699: CryoEM structure of Shaker ILT (V369I,I372L,S376T) -

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Basic information

Entry
Database: EMDB / ID: EMD-74699
TitleCryoEM structure of Shaker ILT (V369I,I372L,S376T)
Map data
Sample
  • Complex: Potassium ion channel with 6 transmembrane helices and T1 domain
    • Protein or peptide: Potassium voltage-gated channel protein Shaker
  • Ligand: POTASSIUM ION
Keywordspotassium ion channel / Triple mutation / Intermediate VSD / Closed state pore / MEMBRANE PROTEIN
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) (fruit fly) / Drosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsAgrawal R / Perozo E / Roux B
Funding support United States, 3 items
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, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74699.png

Downloads & links

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Map

FileDownload / File: emd_74699.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 280 pix.
= 299.04 Å		1.07 Å/pix.
x 280 pix.
= 299.04 Å		1.07 Å/pix.
x 280 pix.
= 299.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.066
Minimum - Maximum-1.1819224 - 1.7767626
Average (Standard dev.)0.00089764287 (±0.02665543)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 299.03998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_74699_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_74699_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Potassium ion channel with 6 transmembrane helices and T1 domain

EntireName: Potassium ion channel with 6 transmembrane helices and T1 domain
Components
  • Complex: Potassium ion channel with 6 transmembrane helices and T1 domain
    • Protein or peptide: Potassium voltage-gated channel protein Shaker
  • Ligand: POTASSIUM ION

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Supramolecule #1: Potassium ion channel with 6 transmembrane helices and T1 domain

SupramoleculeName: Potassium ion channel with 6 transmembrane helices and T1 domain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Drosophila melanogaster (Fruit fly) (fruit fly)
Molecular weightTheoretical: 69 KDa

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Macromolecule #1: Potassium voltage-gated channel protein Shaker

MacromoleculeName: Potassium voltage-gated channel protein Shaker / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 74.296727 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAVAGLYGL GEDRQHRKKQ QQQQQHQKEQ LEQKEEQKKI AERKLQLREQ QLQRNSLDGY GSLPKLSSQD EEGGAGHGFG GGPQHFEPI PHDHDFCERV VINVSGLRFE TQLRTLNQFP DTLLGDPARR LRYFDPLRNE YFFDRSRPSF DAILYYYQSG G RLRRPVNV ...String:
MAAVAGLYGL GEDRQHRKKQ QQQQQHQKEQ LEQKEEQKKI AERKLQLREQ QLQRNSLDGY GSLPKLSSQD EEGGAGHGFG GGPQHFEPI PHDHDFCERV VINVSGLRFE TQLRTLNQFP DTLLGDPARR LRYFDPLRNE YFFDRSRPSF DAILYYYQSG G RLRRPVNV PLDVFSEEIK FYELGDQAIN KFREDEGFIK EEERPLPDNE KQRKVWLLFE YPESSQAARV VAIISVFVIL LS IVIFCLE TLPEFKHYKV FNTTTNGTKI EEDEVPDITD PFFLIETLCI IWFTFELTVR FLACPNKLNF CRDVMNVIDI IAI IPYFIT LATVVAEEED TLNLPKAPVS PQDKSSNQAM SLAILRVIRL VRIFRLFKLT RHSKGLQILG RTLKASMREL GLLI FFLFI GVVLFSSAVY FAEAGSENSF FKSIPDAFWW AVVTMTTVGY GDMTPVGVWG KIVGSLCAIA GVLTIALPVP VIVSN FNYF YHRETDQEEM QSQNFNHVTS CPYLPGTLGQ HMKKSSLSES SSDMMDLDDG VESTPGLTET HPGRSAVAPF LGAQQQ QQQ PVASSLSMSI DKQLQHPLQQ LTQTQLYQQQ QQQQQQQQNG FKQQQQQTQQ QLQQQQSHTI NASAAAATSG SGSSGLT MR HNNALAVSIE TDV

UniProtKB: Potassium voltage-gated channel protein Shaker

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 5 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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

Concentration1 mg/mL
BufferpH: 7.5 / Details: 150mM KCl, 50mM Tris-Cl, 0.02% GDN
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 6600 / Average electron dose: 6.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

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

7sip

Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 293000
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial modelPDB ID:

7sip


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: BACKBONE TRACE
Output model

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

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