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- EMDB-11799: Structure of Human Potassium Chloride Transporter KCC3 S45D/T940D... -

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Basic information

Entry
Database: EMDB / ID: EMD-11799
TitleStructure of Human Potassium Chloride Transporter KCC3 S45D/T940D/T997D in NaCl (Reference Map)
Map data
Sample
  • Complex: Homodimeric complex of human potassium chloride transporter KCC3b
    • Protein or peptide: Isoform 2 of Solute carrier family 12 member 6
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsCCC / transporter / human membrane protein / homodimer / KCC3 / KCC / potassium-chloride coupled transporter / Structural Genomics / Structural Genomics Consortium / SGC / TRANSPORT PROTEIN
Function / homology
Function and homology information


Defective SLC12A6 causes agenesis of the corpus callosum, with peripheral neuropathy (ACCPN) / potassium ion transmembrane transporter activity / potassium:chloride symporter activity / Cation-coupled Chloride cotransporters / chloride ion homeostasis / cellular hypotonic response / cellular hypotonic salinity response / potassium ion homeostasis / cell volume homeostasis / potassium ion import across plasma membrane ...Defective SLC12A6 causes agenesis of the corpus callosum, with peripheral neuropathy (ACCPN) / potassium ion transmembrane transporter activity / potassium:chloride symporter activity / Cation-coupled Chloride cotransporters / chloride ion homeostasis / cellular hypotonic response / cellular hypotonic salinity response / potassium ion homeostasis / cell volume homeostasis / potassium ion import across plasma membrane / monoatomic ion transport / chloride transmembrane transport / potassium ion transmembrane transport / cellular response to glucose stimulus / basolateral plasma membrane / chemical synaptic transmission / angiogenesis / axon / synapse / protein kinase binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
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 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsChi G / Man H
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
European Commission United Kingdom
CitationJournal: EMBO J / Year: 2021
Title: Phospho-regulation, nucleotide binding and ion access control in potassium-chloride cotransporters.
Authors: Gamma Chi / Rebecca Ebenhoch / Henry Man / Haiping Tang / Laurence E Tremblay / Gabriella Reggiano / Xingyu Qiu / Tina Bohstedt / Idlir Liko / Fernando G Almeida / Alexandre P Garneau / Dong ...Authors: Gamma Chi / Rebecca Ebenhoch / Henry Man / Haiping Tang / Laurence E Tremblay / Gabriella Reggiano / Xingyu Qiu / Tina Bohstedt / Idlir Liko / Fernando G Almeida / Alexandre P Garneau / Dong Wang / Gavin McKinley / Christophe P Moreau / Kiran D Bountra / Patrizia Abrusci / Shubhashish M M Mukhopadhyay / Alejandra Fernandez-Cid / Samira Slimani / Julie L Lavoie / Nicola A Burgess-Brown / Ben Tehan / Frank DiMaio / Ali Jazayeri / Paul Isenring / Carol V Robinson / Katharina L Dürr /
Abstract: Potassium-coupled chloride transporters (KCCs) play crucial roles in regulating cell volume and intracellular chloride concentration. They are characteristically inhibited under isotonic conditions ...Potassium-coupled chloride transporters (KCCs) play crucial roles in regulating cell volume and intracellular chloride concentration. They are characteristically inhibited under isotonic conditions via phospho-regulatory sites located within the cytoplasmic termini. Decreased inhibitory phosphorylation in response to hypotonic cell swelling stimulates transport activity, and dysfunction of this regulatory process has been associated with various human diseases. Here, we present cryo-EM structures of human KCC3b and KCC1, revealing structural determinants for phospho-regulation in both N- and C-termini. We show that phospho-mimetic KCC3b is arrested in an inward-facing state in which intracellular ion access is blocked by extensive contacts with the N-terminus. In another mutant with increased isotonic transport activity, KCC1Δ19, this interdomain interaction is absent, likely due to a unique phospho-regulatory site in the KCC1 N-terminus. Furthermore, we map additional phosphorylation sites as well as a previously unknown ATP/ADP-binding pocket in the large C-terminal domain and show enhanced thermal stabilization of other CCCs by adenine nucleotides. These findings provide fundamentally new insights into the complex regulation of KCCs and may unlock innovative strategies for drug development.
History
DepositionSep 28, 2020-
Header (metadata) releaseJun 2, 2021-
Map releaseJun 2, 2021-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ain
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11799.png

Downloads & links

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Map

FileDownload / File: emd_11799.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.)
0.65 Å/pix.
x 400 pix.
= 260.4 Å		0.65 Å/pix.
x 400 pix.
= 260.4 Å		0.65 Å/pix.
x 400 pix.
= 260.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.651 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17 / Movie #1: 0.2
Minimum - Maximum-1.2067341 - 1.7890539
Average (Standard dev.)0.0018878438 (±0.043935217)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 260.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6510.6510.651
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z260.400260.400260.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-1.2071.7890.002

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Supplemental data

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Mask #1

Fileemd_11799_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_11799_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_11799_half_map_2.map
Projections & Slices
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Sample components

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Entire : Homodimeric complex of human potassium chloride transporter KCC3b

EntireName: Homodimeric complex of human potassium chloride transporter KCC3b
Components
  • Complex: Homodimeric complex of human potassium chloride transporter KCC3b
    • Protein or peptide: Isoform 2 of Solute carrier family 12 member 6
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Homodimeric complex of human potassium chloride transporter KCC3b

SupramoleculeName: Homodimeric complex of human potassium chloride transporter KCC3b
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 240 KDa

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Macromolecule #1: Isoform 2 of Solute carrier family 12 member 6

MacromoleculeName: Isoform 2 of Solute carrier family 12 member 6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 122.433297 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPHFTVTKVE DPEEGAAASI SQEPSLADIK ARIQDSDEPD LSQNDITGEH SQLLDDGHKK ARNAYLNNSN YEEGDEYFDK NLALFEEEM DTRPKVSSLL NRMANYTNLT QGAKEHEEAE NITEGKKKPT KTPQMGTFMG VYLPCLQNIF GVILFLRLTW V VGTAGVLQ ...String:
MPHFTVTKVE DPEEGAAASI SQEPSLADIK ARIQDSDEPD LSQNDITGEH SQLLDDGHKK ARNAYLNNSN YEEGDEYFDK NLALFEEEM DTRPKVSSLL NRMANYTNLT QGAKEHEEAE NITEGKKKPT KTPQMGTFMG VYLPCLQNIF GVILFLRLTW V VGTAGVLQ AFAIVLICCC CTMLTAISMS AIATNGVVPA GGSYFMISRA LGPEFGGAVG LCFYLGTTFA AAMYILGAIE IF LVYIVPR AAIFHSDDAL KESAAMLNNM RVYGTAFLVL MVLVVFIGVR YVNKFASLFL ACVIVSILAI YAGAIKSSFA PPH FPVCML GNRTLSSRHI DVCSKTKEIN NMTVPSKLWG FFCNSSQFFN ATCDEYFVHN NVTSIQGIPG LASGIITENL WSNY LPKGE IIEKPSAKSS DVLGSLNHEY VLVDITTSFT LLVGIFFPSV TGIMAGSNRS GDLKDAQKSI PIGTILAILT TSFVY LSNV VLFGACIEGV VLRDKFGDAV KGNLVVGTLS WPSPWVIVIG SFFSTCGAGL QSLTGAPRLL QAIAKDNIIP FLRVFG HSK ANGEPTWALL LTAAIAELGI LIASLDLVAP ILSMFFLMCY LFVNLACALQ TLLRTPNWRP RFRYYHWALS FMGMSIC LA LMFISSWYYA IVAMVIAGMI YKYIEYQGAE KEWGDGIRGL SLSAARFALL RLEEGPPHTK NWRPQLLVLL KLDEDLHV K HPRLL(TPO)FASQ LKAGKGLTIV GSVIVGNFLE NYGEALAAEQ TIKHLMEAEK VKGFCQLVVA AKLREGISHL IQSCG LGGM KHNTVVMGWP NGWRQSEDAR AWKTFIGTVR VTTAAHLALL VAKNISFFPS NVEQFSEGNI DVWWIVHDGG MLMLLP FLL KQHKVWRKCS IRIFTVAQLE DNSIQMKKDL ATFLYHLRIE AEVEVVEMHD (SEP)DISAYTYER DLMMEQRSQM LRH MRLSKT ERDREAQLVK DRNSMLRLTS IGSDEDEETE TYQEKVHMDW TKDKYMASRG QKAKSMEGFQ DLLNMRPDQS NVRR MHTAV KLNEVIVNKS HEAKLVLLNM PGPPRNPEGD ENYMEFLEVL TEGLERVLLV RGGGSEVITI YS

UniProtKB: Solute carrier family 12 member 6

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4053596
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 408039
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6y5r


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsModel from previous map/model repositioned with Chimera and refined with Coot/Phenix.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7ain:
Structure of Human Potassium Chloride Transporter KCC3 S45D/T940D/T997D in NaCl (Reference Map)

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