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- EMDB-26115: Human potassium-chloride cotransporter 1 in inward-open state -

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Basic information

Entry
Database: EMDB / ID: EMD-26115
TitleHuman potassium-chloride cotransporter 1 in inward-open state
Map data
Sample
  • Complex: Human Potassium-chloride cotransporter 1
    • Protein or peptide: Solute carrier family 12 member 4
  • Ligand: POTASSIUM ION
KeywordsSLC12A4 / Potassium-chloride transport / Inward-open state / TRANSPORT PROTEIN
Function / homology
Function and homology information


potassium:chloride symporter activity / Cation-coupled Chloride cotransporters / chloride ion homeostasis / potassium ion homeostasis / cell volume homeostasis / potassium ion import across plasma membrane / monoatomic ion transport / potassium ion transmembrane transport / chloride transmembrane transport / chemical synaptic transmission ...potassium:chloride symporter activity / Cation-coupled Chloride cotransporters / chloride ion homeostasis / potassium ion homeostasis / cell volume homeostasis / potassium ion import across plasma membrane / monoatomic ion transport / potassium ion transmembrane transport / chloride transmembrane transport / chemical synaptic transmission / lysosomal membrane / synapse / protein kinase binding / ATP binding / membrane / plasma membrane
Similarity search - Function
K/Cl co-transporter 1 / K/Cl co-transporter / SLC12A transporter, C-terminal / Solute carrier family 12 / Amino acid permease/ SLC12A domain / SLC12A transporter family / Amino acid permease
Similarity search - Domain/homology
Solute carrier family 12 member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsZhao YX / Cao EH
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Structure of the human cation-chloride cotransport KCC1 in an outward-open state.
Authors: Yongxiang Zhao / Jiemin Shen / Qinzhe Wang / Manuel Jose Ruiz Munevar / Pietro Vidossich / Marco De Vivo / Ming Zhou / Erhu Cao /
Abstract: Cation-chloride cotransporters (CCCs) catalyze electroneutral symport of Cl with Na and/or K across membranes. CCCs are fundamental in cell volume homeostasis, transepithelia ion movement, ...Cation-chloride cotransporters (CCCs) catalyze electroneutral symport of Cl with Na and/or K across membranes. CCCs are fundamental in cell volume homeostasis, transepithelia ion movement, maintenance of intracellular Cl concentration, and neuronal excitability. Here, we present a cryoelectron microscopy structure of human K-Cl cotransporter (KCC)1 bound with the VU0463271 inhibitor in an outward-open state. In contrast to many other amino acid-polyamine-organocation transporter cousins, our first outward-open CCC structure reveals that opening the KCC1 extracellular ion permeation path does not involve hinge-bending motions of the transmembrane (TM) 1 and TM6 half-helices. Instead, rocking of TM3 and TM8, together with displacements of TM4, TM9, and a conserved intracellular loop 1 helix, underlie alternate opening and closing of extracellular and cytoplasmic vestibules. We show that KCC1 intriguingly exists in one of two distinct dimeric states via different intersubunit interfaces. Our studies provide a blueprint for understanding the mechanisms of CCCs and their inhibition by small molecule compounds.
History
DepositionFeb 1, 2022-
Header (metadata) releaseJun 29, 2022-
Map releaseJun 29, 2022-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26115.png

Downloads & links

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Map

FileDownload / File: emd_26115.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 279.552 Å		1.09 Å/pix.
x 256 pix.
= 279.552 Å		1.09 Å/pix.
x 256 pix.
= 279.552 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.092 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-2.5681458 - 4.1487794
Average (Standard dev.)-0.0003586047 (±0.11380874)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 279.552 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_26115_additional_1.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 : Human Potassium-chloride cotransporter 1

EntireName: Human Potassium-chloride cotransporter 1
Components
  • Complex: Human Potassium-chloride cotransporter 1
    • Protein or peptide: Solute carrier family 12 member 4
  • Ligand: POTASSIUM ION

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Supramolecule #1: Human Potassium-chloride cotransporter 1

SupramoleculeName: Human Potassium-chloride cotransporter 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 12 member 4

MacromoleculeName: Solute carrier family 12 member 4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 120.770492 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPHFTVVPVD GPRRGDYDNL EGLSWVDYGE RAELDDSDGH GNHRESSPFL SPLEASRGID YYDRNLALFE EELDIRPKVS SLLGKLVSY TNLTQGAKEH EEAESGEGTR RRAAEAPSMG TLMGVYLPCL QNIFGVILFL RLTWMVGTAG VLQALLIVLI C CCCTLLTA ...String:
MPHFTVVPVD GPRRGDYDNL EGLSWVDYGE RAELDDSDGH GNHRESSPFL SPLEASRGID YYDRNLALFE EELDIRPKVS SLLGKLVSY TNLTQGAKEH EEAESGEGTR RRAAEAPSMG TLMGVYLPCL QNIFGVILFL RLTWMVGTAG VLQALLIVLI C CCCTLLTA ISMSAIATNG VVPAGGSYFM ISRSLGPEFG GAVGLCFYLG TTFAAAMYIL GAIEILLTYI APPAAIFYPS GA HDTSNAT LNNMRVYGTI FLTFMTLVVF VGVKYVNKFA SLFLACVIIS ILSIYAGGIK SIFDPPVFPV CMLGNRTLSR DQF DICAKT AVVDNETVAT QLWSFFCHSP NLTTDSCDPY FMLNNVTEIP GIPGAAAGVL QENLWSAYLE KGDIVEKHGL PSAD APSLK ESLPLYVVAD IATSFTVLVG IFFPSVTGIM AGSNRSGDLR DAQKSIPVGT ILAIITTSLV YFSSVVLFGA CIEGV VLRD KYGDGVSRNL VVGTLAWPSP WVIVIGSFFS TCGAGLQSLT GAPRLLQAIA KDNIIPFLRV FGHGKVNGEP TWALLL TAL IAELGILIAS LDMVAPILSM FFLMCYLFVN LACAVQTLLR TPNWRPRFKY YHWALSFLGM SLCLALMFVS SWYYALV AM LIAGMIYKYI EYQGAEKEWG DGIRGLSLSA ARYALLRLEE GPPHTKNWRP QLLVLLKLDE DLHVKYPRLL TFASQLKA G KGLTIVGSVI QGSFLESYGE AQAAEQTIKN MMEIEKVKGF CQVVVASKVR EGLAHLIQSC GLGGMRHNSV VLGWPYGWR QSEDPRAWKT FIDTVRCTTA AHLALLVPKN IAFYPSNHER YLEGHIDVWW IVHDGGMLML LPFLLRQHKV WRKCRMRIFT VAQMDDNSI QMKKDLAVFL YHLRLEAEVE VVEMHNSDIS AYTYERTLMM EQRSQMLRQM RLTKTERERE AQLVKDRHSA L RLESLYSD EEDESAVGAD KIQMTWTRDK YMTETWDPSH APDNFRELVH IKPDQSNVRR MHTAVKLNEV IVTRSHDARL VL LNMPGPP RNSEGDENYM EFLEVLTEGL ERVLLVRGGG REVITIYS

UniProtKB: Solute carrier family 12 member 4

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Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 2 / 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4073077
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Number images used: 79153
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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