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- EMDB-30615: human potassium-chloride co-transporter KCC2 -

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Basic information

Entry
Database: EMDB / ID: EMD-30615
Titlehuman potassium-chloride co-transporter KCC2
Map data
Sample
  • Complex: potassium-chloride cotransporter 2
    • Protein or peptide: potassium-chloride cotransporter 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordspotassium-chloride / co-transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


thermosensory behavior / intracellular pH reduction / plasma membrane => GO:0005886 / potassium:chloride symporter activity / Cation-coupled Chloride cotransporters / hypotonic response / intracellular chloride ion homeostasis / intracellular monoatomic ion homeostasis / ammonium channel activity / chloride ion homeostasis ...thermosensory behavior / intracellular pH reduction / plasma membrane => GO:0005886 / potassium:chloride symporter activity / Cation-coupled Chloride cotransporters / hypotonic response / intracellular chloride ion homeostasis / intracellular monoatomic ion homeostasis / ammonium channel activity / chloride ion homeostasis / dendritic spine development / potassium ion homeostasis / cell volume homeostasis / chloride transmembrane transporter activity / potassium ion import across plasma membrane / membrane => GO:0016020 / monoatomic ion transport / chloride transmembrane transport / dendrite membrane / learning / cell periphery / multicellular organism growth / chemical synaptic transmission / perikaryon / neuron projection / response to xenobiotic stimulus / neuronal cell body / synapse / protein kinase binding / plasma membrane
Similarity search - Function
K/Cl co-transporter 2 / 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 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsXie Y / Chang S
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870724 China
CitationJournal: Sci Adv / Year: 2020
Title: Structures and an activation mechanism of human potassium-chloride cotransporters.
Authors: Yuan Xie / Shenghai Chang / Cheng Zhao / Feng Wang / Si Liu / Jin Wang / Eric Delpire / Sheng Ye / Jiangtao Guo /
Abstract: Potassium-chloride cotransporters KCC1 to KCC4 mediate the coupled export of potassium and chloride across the plasma membrane and play important roles in cell volume regulation, auditory system ...Potassium-chloride cotransporters KCC1 to KCC4 mediate the coupled export of potassium and chloride across the plasma membrane and play important roles in cell volume regulation, auditory system function, and γ-aminobutyric acid (GABA) and glycine-mediated inhibitory neurotransmission. Here, we present 2.9- to 3.6-Å resolution structures of full-length human KCC2, KCC3, and KCC4. All three KCCs adopt a similar overall architecture, a domain-swap dimeric assembly, and an inward-facing conformation. The structural and functional studies reveal that one unexpected N-terminal peptide binds at the cytosolic facing cavity and locks KCC2 and KCC4 at an autoinhibition state. The C-terminal domain (CTD) directly interacts with the N-terminal inhibitory peptide, and the relative motions between the CTD and the transmembrane domain (TMD) suggest that CTD regulates KCCs' activities by adjusting the autoinhibitory effect. These structures provide the first glimpse of full-length structures of KCCs and an autoinhibition mechanism among the amino acid-polyamine-organocation transporter superfamily.
History
DepositionOct 11, 2020-
Header (metadata) releaseDec 30, 2020-
Map releaseDec 30, 2020-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7d8z
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30615.png

Downloads & links

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Map

FileDownload / File: emd_30615.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 240 pix.
= 243.36 Å		1.01 Å/pix.
x 240 pix.
= 243.36 Å		1.01 Å/pix.
x 240 pix.
= 243.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014 / Movie #1: 0.014
Minimum - Maximum-0.03644505 - 0.05754394
Average (Standard dev.)-0.0000021889648 (±0.0027344394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 243.36002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z243.360243.360243.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0360.058-0.000

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Supplemental data

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Sample components

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Entire : potassium-chloride cotransporter 2

EntireName: potassium-chloride cotransporter 2
Components
  • Complex: potassium-chloride cotransporter 2
    • Protein or peptide: potassium-chloride cotransporter 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: potassium-chloride cotransporter 2

SupramoleculeName: potassium-chloride cotransporter 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: potassium-chloride cotransporter 2

MacromoleculeName: potassium-chloride cotransporter 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 128.486414 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKM SRRFTVTSLP PAGPARSPDP ESRRHSVADP RHLPGEDVKG DGNPKESSPF INSTDTEKGK EYDGKNMALF EEEMDTSPM VSSLLSGLAN YTNLPQGSRE HEEAENNEGG KKKPVQAPRM GTFMGVYLPC LQNIFGVILF LRLTWVVGIA G IMESFCMV ...String:
MDYKDDDDKM SRRFTVTSLP PAGPARSPDP ESRRHSVADP RHLPGEDVKG DGNPKESSPF INSTDTEKGK EYDGKNMALF EEEMDTSPM VSSLLSGLAN YTNLPQGSRE HEEAENNEGG KKKPVQAPRM GTFMGVYLPC LQNIFGVILF LRLTWVVGIA G IMESFCMV FICCSCTMLT AISMSAIATN GVVPAGGSYY MISRSLGPEF GGAVGLCFYL GTTFAGAMYI LGTIEILLAY LF PAMAIFK AEDASGEAAA MLNNMRVYGT CVLTCMATVV FVGVKYVNKF ALVFLGCVIL SILAIYAGVI KSAFDPPNFP ICL LGNRTL SRHGFDVCAK LAWEGNETVT TRLWGLFCSS RFLNATCDEY FTRNNVTEIQ GIPGAASGLI KENLWSSYLT KGVI VERSG MTSVGLADGT PIDMDHPYVF SDMTSYFTLL VGIYFPSVTG IMAGSNRSGD LRDAQKSIPT GTILAIATTS AVYIS SVVL FGACIEGVVL RDKFGEAVNG NLVVGTLAWP SPWVIVIGSF FSTCGAGLQS LTGAPRLLQA ISRDGIVPFL QVFGHG KAN GEPTWALLLT ACICEIGILI ASLDEVAPIL SMFFLMCYMF VNLACAVQTL LRTPNWRPRF RYYHWTLSFL GMSLCLA LM FICSWYYALV AMLIAGLIYK YIEYRGAEKE WGDGIRGLSL SAARYALLRL EEGPPHTKNW RPQLLVLVRV DQDQNVVH P QLLSLTSQLK AGKGLTIVGS VLEGTFLENH PQAQRAEESI RRLMEAEKVK GFCQVVISSN LRDGVSHLIQ SGGLGGLQH NTVLVGWPRN WRQKEDHQTW RNFIELVRET TAGHLALLVT KNVSMFPGNP ERFSEGSIDV WWIVHDGGML MLLPFLLRHH KVWRKCKMR IFTVAQMDDN SIQMKKDLTT FLYHLRITAE VEVVEMHESD ISAYTYEKTL VMEQRSQILK QMHLTKNERE R EIQSITDE SRGSIRRKNP ANTRLRLNVP EETAGDSEEK PEEEVQLIHD QSAPSCPSSS PSPGEEPEGE GETDPEKVHL TW TKDKSVA EKNKGPSPVS SEGIKDFFSM KPEWENLNQS NVRRMHTAVR LNEVIVKKSR DAKLVLLNMP GPPRNRNGDE NYM EFLEVL TEHLDRVMLV RGGGREVITI YSWSHPQFEK

UniProtKB: Solute carrier family 12 member 5

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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: 4 / 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: 8
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: 62.0 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55026
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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