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- EMDB-30617: human potassium-chloride co-transporter KCC4 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-30617
Titlehuman potassium-chloride co-transporter KCC4
Map data
Sample
  • Complex: potassium-chloride cotransporter 4
    • Protein or peptide: potassium-chloride co-transporter KCC4
  • Ligand: POTASSIUM IONPotassium
  • Ligand: CHLORIDE IONChloride
Function / homology
Function and homology information


ammonium import across plasma membrane / potassium:chloride symporter activity / Cation-coupled Chloride cotransporters / chloride ion homeostasis / ammonium transmembrane transporter activity / potassium ion homeostasis / cell volume homeostasis / potassium ion import across plasma membrane / plasma membrane => GO:0005886 / monoatomic ion transport ...ammonium import across plasma membrane / potassium:chloride symporter activity / Cation-coupled Chloride cotransporters / chloride ion homeostasis / ammonium transmembrane transporter activity / potassium ion homeostasis / cell volume homeostasis / potassium ion import across plasma membrane / plasma membrane => GO:0005886 / monoatomic ion transport / chloride transmembrane transport / chemical synaptic transmission / synapse / protein kinase binding / protein-containing complex / plasma membrane
Similarity search - Function
K/Cl co-transporter 4 / K/Cl co-transporter / SLC12A transporter family / SLC12A transporter, C-terminal / Solute carrier family 12 / Amino acid permease/ SLC12A domain / Amino acid permease
Similarity search - Domain/homology
Solute carrier family 12 member 7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsXie Y / Chang S / Zhao C / Ye S / Guo J
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 12, 2020-
Header (metadata) releaseDec 30, 2020-
Map releaseDec 30, 2020-
UpdateDec 30, 2020-
Current statusDec 30, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7d99
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30617.png

Downloads & links

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Map

FileDownload / File: emd_30617.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.014 Å
Density
Contour LevelBy AUTHOR: 0.023 / Movie #1: 0.023
Minimum - Maximum-0.10115795 - 0.17242338
Average (Standard dev.)2.788134e-05 (±0.005600522)
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-0.1010.1720.000

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Supplemental data

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Sample components

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Entire : potassium-chloride cotransporter 4

EntireName: potassium-chloride cotransporter 4
Components
  • Complex: potassium-chloride cotransporter 4
    • Protein or peptide: potassium-chloride co-transporter KCC4
  • Ligand: POTASSIUM IONPotassium
  • Ligand: CHLORIDE IONChloride

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Supramolecule #1: potassium-chloride cotransporter 4

SupramoleculeName: potassium-chloride cotransporter 4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293T

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Macromolecule #1: potassium-chloride co-transporter KCC4

MacromoleculeName: potassium-chloride co-transporter KCC4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 123.069492 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKH HHHHHENLYF QGMPTNFTVV PVEAHADGGG DETAERTEAP GTPEGPEPER PSPGDGNPRE NSPFLNNVEV EQESFFEGK NMALFEEEMD SNPMVSSLLN KLANYTNLSQ GVVEHEEDEE SRRREAKAPR MGTFIGVYLP CLQNILGVIL F LRLTWIVG ...String:
MDYKDDDDKH HHHHHENLYF QGMPTNFTVV PVEAHADGGG DETAERTEAP GTPEGPEPER PSPGDGNPRE NSPFLNNVEV EQESFFEGK NMALFEEEMD SNPMVSSLLN KLANYTNLSQ GVVEHEEDEE SRRREAKAPR MGTFIGVYLP CLQNILGVIL F LRLTWIVG VAGVLESFLI VAMCCTCTML TAISMSAIAT NGVVPAGGSY YMISRSLGPE FGGAVGLCFY LGTTFAGAMY IL GTIEIFL TYISPGAAIF QAEAAGGEAA AMLHNMRVYG TCTLVLMALV VFVGVKYVNK LALVFLACVV LSILAIYAGV IKS AFDPPD IPVCLLGNRT LSRRSFDACV KAYGIHNNSA TSALWGLFCN GSQPSAACDE YFIQNNVTEI QGIPGAASGV FLEN LWSTY AHAGAFVEKK GVPSVPVAEE SRASALPYVL TDIAASFTLL VGIYFPSVTG IMAGSNRSGD LKDAQKSIPT GTILA IVTT SFIYLSCIVL FGACIEGVVL RDKFGEALQG NLVIGMLAWP SPWVIVIGSF FSTCGAGLQS LTGAPRLLQA IARDGI VPF LQVFGHGKAN GEPTWALLLT VLICETGILI ASLDSVAPIL SMFFLMCYLF VNLACAVQTL LRTPNWRPRF KFYHWTL SF LGMSLCLALM FICSWYYALS AMLIAGCIYK YIEYRGAEKE WGDGIRGLSL NAARYALLRV EHGPPHTKNW RPQVLVML N LDAEQAVKHP RLLSFTSQLK AGKGLTIVGS VLEGTYLDKH MEAQRAEENI RSLMSTEKTK GFCQLVVSSS LRDGMSHLI QSAGLGGLKH NTVLMAWPAS WKQEDNPFSW KNFVDTVRDT TAAHQALLVA KNVDSFPQNQ ERFGGGHIDV WWIVHDGGML MLLPFLLRQ HKVWRKCRMR IFTVAQVDDN SIQMKKDLQM FLYHLRISAE VEVVEMVEND ISAFTYERTL MMEQRSQMLK Q MQLSKNEQ EREAQLIHDR NTASHTAAAA RTQAPPTPDK VQMTWTREKL IAEKYRSRDT SLSGFKDLFS MKPDQSNVRR MH TAVKLNG VVLNKSQDAQ LVLLNMPGPP KNRQGDENYM EFLEVLTEGL NRVLLVRGGG REVITIYSWS HPQFEK

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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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Macromolecule #4: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: CL
Molecular weightTheoretical: 35.453 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 62.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 95572

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