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- PDB-9rnj: Cryo-EM structure of the human potassium chloride cotransporter T... -

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Basic information

Entry
Database: PDB / ID: 9rnj
TitleCryo-EM structure of the human potassium chloride cotransporter T906A/T1007A phospho-knockout mutants KCC2b bound ATP in LMNG (outward-facing state, dimer)
ComponentsIsoform 2 of Solute carrier family 12 member 5
KeywordsMEMBRANE PROTEIN / Transporter / Cation/chloride cotransporter
Function / homology
Function and homology information


thermosensory behavior / intracellular pH reduction / potassium:chloride symporter activity / hypotonic response / Cation-coupled Chloride cotransporters / intracellular chloride ion homeostasis / ammonium channel activity / chloride ion homeostasis / dendritic spine development / postsynaptic neurotransmitter receptor diffusion trapping ...thermosensory behavior / intracellular pH reduction / potassium:chloride symporter activity / hypotonic response / Cation-coupled Chloride cotransporters / intracellular chloride ion homeostasis / ammonium channel activity / chloride ion homeostasis / dendritic spine development / postsynaptic neurotransmitter receptor diffusion trapping / potassium ion homeostasis / cell volume homeostasis / chloride transmembrane transporter activity / postsynaptic specialization membrane / potassium ion import across plasma membrane / regulation of postsynapse assembly / monoatomic ion transport / dendrite membrane / chloride transmembrane transport / cell periphery / learning / multicellular organism growth / chemical synaptic transmission / perikaryon / neuron projection / response to xenobiotic stimulus / neuronal cell body / protein kinase binding / glutamatergic synapse / membrane / metal ion binding / plasma membrane
Similarity search - Function
K/Cl co-transporter / SLC12A transporter, C-terminal / Solute carrier family 12 / SLC12A transporter family / Amino acid permease/ SLC12A domain / Amino acid permease
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Chem-JUX / Solute carrier family 12 member 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsMatsuoka, R. / Oswald, C. / Jazayeri, A. / Duerr, K.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Distinct cytoplasmic domain interactions control autoinhibition of the neuronal potassium coupled chloride transporter KCC2
Authors: Matsuoka, R. / Oswald, C. / Jazayeri, A. / Duerr, K.L.
History
DepositionJun 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
B: Isoform 2 of Solute carrier family 12 member 5
A: Isoform 2 of Solute carrier family 12 member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,06212
Polymers258,1202
Non-polymers1,94210
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Isoform 2 of Solute carrier family 12 member 5 / Electroneutral potassium-chloride cotransporter 2 / K-Cl cotransporter 2 / hKCC2 / Neuronal K-Cl cotransporter


Mass: 129059.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC12A5, KCC2, KIAA1176 / Production host: Homo sapiens (human) / References: UniProt: Q9H2X9

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Non-polymers , 5 types, 12 molecules

#2: Chemical ChemComp-JUX / N-cyclopropyl-N-(4-methyl-1,3-thiazol-2-yl)-2-[(6-phenylpyridazin-3-yl)sulfanyl]acetamide


Mass: 382.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H18N4OS2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

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: Dimer structure of KCC2 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 6.8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisTris-HCl1
2100 mMsodium chlorideNaCl1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 269 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingAverage exposure time: 2 sec. / Electron dose: 42 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 5002
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
2PHENIXdev_5407model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44814 / Symmetry type: POINT
RefinementHighest resolution: 3.86 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00214504
ELECTRON MICROSCOPYf_angle_d0.49219698
ELECTRON MICROSCOPYf_dihedral_angle_d9.7995268
ELECTRON MICROSCOPYf_chiral_restr0.0382252
ELECTRON MICROSCOPYf_plane_restr0.0042476

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