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- EMDB-30543: Mouse KCC2 -

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Basic information

Entry
Database: EMDB / ID: EMD-30543
TitleMouse KCC2
Map data
Sample
  • Organelle or cellular component: mouse KCC2
    • Protein or peptide: Solute carrier family 12 member 5
Keywordstransporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


Cation-coupled Chloride cotransporters / thermosensory behavior / intracellular pH reduction / hypotonic response / potassium:chloride symporter activity / intracellular chloride ion homeostasis / ammonium channel activity / dendritic spine development / postsynaptic neurotransmitter receptor diffusion trapping / chloride transport ...Cation-coupled Chloride cotransporters / thermosensory behavior / intracellular pH reduction / hypotonic response / potassium:chloride symporter activity / intracellular chloride ion homeostasis / ammonium channel activity / dendritic spine development / postsynaptic neurotransmitter receptor diffusion trapping / chloride transport / postsynaptic specialization membrane / regulation of postsynapse assembly / monoatomic ion transport / potassium ion transmembrane transport / dendrite membrane / dendritic shaft / cell periphery / learning / multicellular organism growth / perikaryon / chemical synaptic transmission / response to xenobiotic stimulus / neuronal cell body / glutamatergic synapse / metal ion binding / membrane / 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
Solute carrier family 12 member 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsZhang S / Yang M
CitationJournal: Commun Biol / Year: 2021
Title: The structural basis of function and regulation of neuronal cotransporters NKCC1 and KCC2.
Authors: Sensen Zhang / Jun Zhou / Yuebin Zhang / Tianya Liu / Perrine Friedel / Wei Zhuo / Suma Somasekharan / Kasturi Roy / Laixing Zhang / Yang Liu / Xianbin Meng / Haiteng Deng / Wenwen Zeng / ...Authors: Sensen Zhang / Jun Zhou / Yuebin Zhang / Tianya Liu / Perrine Friedel / Wei Zhuo / Suma Somasekharan / Kasturi Roy / Laixing Zhang / Yang Liu / Xianbin Meng / Haiteng Deng / Wenwen Zeng / Guohui Li / Biff Forbush / Maojun Yang /
Abstract: NKCC and KCC transporters mediate coupled transport of Na+K+Cl and K+Cl across the plasma membrane, thus regulating cell Cl concentration and cell volume and playing critical roles in transepithelial ...NKCC and KCC transporters mediate coupled transport of Na+K+Cl and K+Cl across the plasma membrane, thus regulating cell Cl concentration and cell volume and playing critical roles in transepithelial salt and water transport and in neuronal excitability. The function of these transporters has been intensively studied, but a mechanistic understanding has awaited structural studies of the transporters. Here, we present the cryo-electron microscopy (cryo-EM) structures of the two neuronal cation-chloride cotransporters human NKCC1 (SLC12A2) and mouse KCC2 (SLC12A5), along with computational analysis and functional characterization. These structures highlight essential residues in ion transport and allow us to propose mechanisms by which phosphorylation regulates transport activity.
History
DepositionSep 13, 2020-
Header (metadata) releaseApr 14, 2021-
Map releaseApr 14, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7d14
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30543.png

Downloads & links

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Map

FileDownload / File: emd_30543.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 349.12 Å		1.09 Å/pix.
x 320 pix.
= 349.12 Å		1.09 Å/pix.
x 320 pix.
= 349.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.091 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.024 / Movie #1: 0.024
Minimum - Maximum-0.0513047 - 0.08950083
Average (Standard dev.)0.00019440474 (±0.001956037)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 349.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z349.120349.120349.120
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0510.0900.000

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Supplemental data

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Sample components

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Entire : mouse KCC2

EntireName: mouse KCC2
Components
  • Organelle or cellular component: mouse KCC2
    • Protein or peptide: Solute carrier family 12 member 5

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Supramolecule #1: mouse KCC2

SupramoleculeName: mouse KCC2 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Solute carrier family 12 member 5

MacromoleculeName: Solute carrier family 12 member 5 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 126.402328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSRRFTVTSL PPAASAASAD PESRRHSVAD PRRLPREDVK GDGNPKESSP FINSTDTEKG REYDGRNMAL FEEEMDTSPM VSSLLSGLA NYTNLPQGSR EHEEAENNEG GKKKPVQAPR MGTFMGVYLP CLQNIFGVIL FLRLTWVVGI AGIMESFCMV F ICCSCTML ...String:
MSRRFTVTSL PPAASAASAD PESRRHSVAD PRRLPREDVK GDGNPKESSP FINSTDTEKG REYDGRNMAL FEEEMDTSPM VSSLLSGLA NYTNLPQGSR EHEEAENNEG GKKKPVQAPR MGTFMGVYLP CLQNIFGVIL FLRLTWVVGI AGIMESFCMV F ICCSCTML TAISMSAIAT NGVVPAGGSY YMISRSLGPE FGGAVGLCFY LGTTFAGAMY ILGTIEILLA YLFPAMAIFK AE DASGEAA AMLNNMRVYG TCVLTCMATV VFVGVKYVNK FALVFLGCVI LSILAIYAGV IKSAFDPPNF PICLLGNRTL SRH GFDVCA KLAWEGNETV TTRLWGLFCS SRLLNATCDE YFTRNNVTEI QGIPGAASGL IKENLWSSYL TKGVIVERRG MPSV GLADG TPVDMDHPYV FSDMTSYFTL LVGIYFPSVT GIMAGSNRSG DLRDAQKSIP TGTILAIATT SAVYISSVVL FGACI EGVV LRDKFGEAVN GNLVVGTLAW PSPWVIVIGS FFSTCGAGLQ SLTGAPRLLQ AISRDGIVPF LQVFGHGKAN GEPTWA LLL TACICEIGIL IASLDEVAPI LSMFFLMCYM FVNLACAVQT LLRTPNWRPR FRYYHWTLSF LGMSLCLALM FICSWYY AL VAMLIAGLIY KYIEYRGAEK EWGDGIRGLS LSAARYALLR LEEGPPHTKN WRPQLLVLVR VDQDQNVVHP QLLSLTSQ L KAGKGLTIVG SVLEGTFLDN HPQAQRAEES IRRLMEAEKV KGFCQVVISS NLRDGVSHLI QSGGLGGLQH NTVLVGWPR NWRQKEDHQT WRNFIELVRE TTAGHLALLV TKNVSMFPGN PERFSEGSID VWWIVHDGGM LMLLPFLLRH HKVWRKCKMR IFTVAQMDD NSIQMKKDLT TFLYHLRITA EVEVVEMHES DISAYTYEKT LVMEQRSQIL KQMHLTKNER EREIQSITDE S RGSIRRKN PANPRLRLNV PEETACDNEE KPEEEVQLIH DQSAPSCPSS SPSPGEEPEG ERETDPEVHL TWTKDKSVAE KN KGPSPVS SEGIKDFFSM KPEWENLNQS NVRRMHTAVR LNEVIVNKSR DAKLVLLNMP GPPRNRNGDE NYMEFLEVLT EQL DRVMLV RGGGREVITI YS

UniProtKB: Solute carrier family 12 member 5

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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 K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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