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- EMDB-75588: Cryo-EM structure of a bovine CLC-K S68N/R355K chloride channel w... -

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Basic information

Entry
Database: EMDB / ID: EMD-75588
TitleCryo-EM structure of a bovine CLC-K S68N/R355K chloride channel with inhibitor M-BIM15
Map data
Sample
  • Complex: bovine CLC-K S68N/R355K chloride channel with inhibitor BIM15
    • Protein or peptide: Chloride voltage-gated channel Ka
  • Ligand: (1M)-6-chloro-1-(3-chloro[1,1'-biphenyl]-4-yl)-1H-1,3-benzimidazole-2-sulfonic acid
  • Ligand: CHLORIDE ION
Keywordschloride channel / membrane protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


Stimuli-sensing channels / voltage-gated chloride channel activity / chloride transport / chloride channel complex / basolateral plasma membrane / metal ion binding / plasma membrane
Similarity search - Function
Chloride channel ClC-K / : / Chloride channel, voltage gated / Chloride channel, core / Voltage gated chloride channel / CBS domain superfamily
Similarity search - Domain/homology
Chloride voltage-gated channel Ka
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsChien C-T / Chiu W / Maduke M
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK128881 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM150905 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2026
Title: Mechanism of gating and isoform-specific inhibition in renal CLC chloride channels
Authors: Chien CT / Sobecks-Doherty BL / Powers AS / Das A / Kreiter J / Barry CN / Chen M / Hinman A / Petrakian CF / Williams B / Wood CAP / Xu M / Dror RO / Chiu W / Maduke M
History
DepositionFeb 13, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75588.png

Downloads & links

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Map

FileDownload / File: emd_75588.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 400 pix.
= 296.4 Å		0.74 Å/pix.
x 400 pix.
= 296.4 Å		0.74 Å/pix.
x 400 pix.
= 296.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.741 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.221
Minimum - Maximum-0.36558104 - 0.92817175
Average (Standard dev.)0.0040553347 (±0.027135843)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 296.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_75588_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_75588_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 : bovine CLC-K S68N/R355K chloride channel with inhibitor BIM15

EntireName: bovine CLC-K S68N/R355K chloride channel with inhibitor BIM15
Components
  • Complex: bovine CLC-K S68N/R355K chloride channel with inhibitor BIM15
    • Protein or peptide: Chloride voltage-gated channel Ka
  • Ligand: (1M)-6-chloro-1-(3-chloro[1,1'-biphenyl]-4-yl)-1H-1,3-benzimidazole-2-sulfonic acid
  • Ligand: CHLORIDE ION

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Supramolecule #1: bovine CLC-K S68N/R355K chloride channel with inhibitor BIM15

SupramoleculeName: bovine CLC-K S68N/R355K chloride channel with inhibitor BIM15
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bos taurus (domestic cattle)

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Macromolecule #1: Chloride voltage-gated channel Ka

MacromoleculeName: Chloride voltage-gated channel Ka / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 73.520492 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRVRRGIRGG LDWLKRKLFC VGEDWYFLTV LGVLMALISF TMNFTVGRVV RAHKWLYREI GDSHLLRYLS WTVYPVALVS FSSGFSQSI TPFSGGSGIP ELKTILSGVV LEDYLDIKNF GAKAVGLTCT LASGSTIFLG KVGPFVHLSV MIAAYLGRVR A KATGESEN ...String:
MRVRRGIRGG LDWLKRKLFC VGEDWYFLTV LGVLMALISF TMNFTVGRVV RAHKWLYREI GDSHLLRYLS WTVYPVALVS FSSGFSQSI TPFSGGSGIP ELKTILSGVV LEDYLDIKNF GAKAVGLTCT LASGSTIFLG KVGPFVHLSV MIAAYLGRVR A KATGESEN KSKRNEMLVA GAAVGVATVF AAPFSGVLFC IEVVSSHFSV WDYWRGFFAA TCGAFMFRLL AVFNSEQETI TS LYKTSFR VEVPFDLPEI FFFVALGAIC GVASCAYLFC QRKFLGFVKT NPVLSKLMAT SKPLYSALAA LVLASVTYPP GAG RFMASR LSMKEYLDSL LDHNSWALLT RQASPPWPVE PDPQNLWFEW YHPQFTIFGT LAFFLVMKFW MLILATTIPM PAGY FMPIF IFGAAIGRLL GEALSVAFPE GIVAGGVTNP IMPGGYALAG AAAFSGAVTH SISTALLAFE LTGQIVHALP VLMAV LAAN AIAQSCQPSF YDGTIIVKKL PYLPWIRGRK ISSHRVTVEH FMNRAITTLA KDTPQEEVVK VVTSTDMAEY PLVAST ESQ TLVGTMRRAQ LVQALQAEPP SWAPGQQRCL QDILAEGCPV EPVTLKLSPE TSLHQAHNLF ELLNLQSLFV TSQGRAV GF VSWVELEKAI SKLTNPPAPK SNSLEVLFQ

UniProtKB: Chloride voltage-gated channel Ka

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Macromolecule #2: (1M)-6-chloro-1-(3-chloro[1,1'-biphenyl]-4-yl)-1H-1,3-benzimidazo...

MacromoleculeName: (1M)-6-chloro-1-(3-chloro[1,1'-biphenyl]-4-yl)-1H-1,3-benzimidazole-2-sulfonic acid
type: ligand / ID: 2 / Number of copies: 2 / Formula: A1C8L
Molecular weightTheoretical: 419.281 Da

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Macromolecule #3: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: CL
Molecular weightTheoretical: 35.453 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

BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
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: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 271313
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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