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- EMDB-30058: KCC3 bound with DIOA -

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Basic information

Entry
Database: EMDB / ID: EMD-30058
TitleKCC3 bound with DIOA
Map datacryo_EM map of KCC3 bound with DIOA
Sample
  • Complex: KCC3 bound with DIOA
    • Protein or peptide: Solute carrier family 12 member 6
  • Ligand: POTASSIUM IONPotassium
  • Ligand: CHLORIDE IONChloride
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 2-[[(2~{R})-2-butyl-6,7-bis(chloranyl)-2-cyclopentyl-1-oxidanylidene-3~{H}-inden-5-yl]oxy]ethanoic acid
  • Ligand: water
Function / homology
Function and homology information


Defective SLC12A6 causes agenesis of the corpus callosum, with peripheral neuropathy (ACCPN) / ammonium import across plasma membrane / potassium ion transmembrane transporter activity / potassium:chloride symporter activity / Cation-coupled Chloride cotransporters / chloride ion homeostasis / cellular hypotonic response / ammonium transmembrane transporter activity / cellular hypotonic salinity response / potassium ion homeostasis ...Defective SLC12A6 causes agenesis of the corpus callosum, with peripheral neuropathy (ACCPN) / ammonium import across plasma membrane / potassium ion transmembrane transporter activity / potassium:chloride symporter activity / Cation-coupled Chloride cotransporters / chloride ion homeostasis / cellular hypotonic response / ammonium transmembrane transporter activity / cellular hypotonic salinity response / potassium ion homeostasis / cell volume homeostasis / potassium ion import across plasma membrane / monoatomic ion transport / potassium ion transmembrane transport / chloride transmembrane transport / cellular response to glucose stimulus / chemical synaptic transmission / basolateral plasma membrane / angiogenesis / axon / synapse / protein kinase binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
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 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsChi XM / Li XR / Chen Y / Zhang YY / Su Q / Zhou Q
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971123 China
National Natural Science Foundation of China (NSFC)81920108015 China
National Natural Science Foundation of China (NSFC)31930059 China
CitationJournal: Cell Res / Year: 2021
Title: Cryo-EM structures of the full-length human KCC2 and KCC3 cation-chloride cotransporters.
Authors: Ximin Chi / Xiaorong Li / Yun Chen / Yuanyuan Zhang / Qiang Su / Qiang Zhou /
History
DepositionFeb 26, 2020-
Header (metadata) releaseNov 4, 2020-
Map releaseNov 4, 2020-
UpdateMay 19, 2021-
Current statusMay 19, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6m22
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30058.png

Downloads & links

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Map

FileDownload / File: emd_30058.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo_EM map of KCC3 bound with DIOA
Voxel sizeX=Y=Z: 1.087 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.025
Minimum - Maximum-0.06867914 - 0.16116068
Average (Standard dev.)7.51686e-05 (±0.003172606)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 347.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0871.0871.087
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z347.840347.840347.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0690.1610.000

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Supplemental data

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Sample components

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Entire : KCC3 bound with DIOA

EntireName: KCC3 bound with DIOA
Components
  • Complex: KCC3 bound with DIOA
    • Protein or peptide: Solute carrier family 12 member 6
  • Ligand: POTASSIUM IONPotassium
  • Ligand: CHLORIDE IONChloride
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 2-[[(2~{R})-2-butyl-6,7-bis(chloranyl)-2-cyclopentyl-1-oxidanylidene-3~{H}-inden-5-yl]oxy]ethanoic acid
  • Ligand: water

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Supramolecule #1: KCC3 bound with DIOA

SupramoleculeName: KCC3 bound with DIOA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Macromolecule #1: Solute carrier family 12 member 6

MacromoleculeName: 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: 123.717906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADYKDDDDK SGRMPHFTVT KVEDPEEGAA ASISQEPSLA DIKARIQDSD EPDLSQNSIT GEHSQLLDDG HKKARNAYLN NSNYEEGDE YFDKNLALFE EEMDTRPKVS SLLNRMANYT NLTQGAKEHE EAENITEGKK KPTKTPQMGT FMGVYLPCLQ N IFGVILFL ...String:
MADYKDDDDK SGRMPHFTVT KVEDPEEGAA ASISQEPSLA DIKARIQDSD EPDLSQNSIT GEHSQLLDDG HKKARNAYLN NSNYEEGDE YFDKNLALFE EEMDTRPKVS SLLNRMANYT NLTQGAKEHE EAENITEGKK KPTKTPQMGT FMGVYLPCLQ N IFGVILFL RLTWVVGTAG VLQAFAIVLI CCCCTMLTAI SMSAIATNGV VPAGGSYFMI SRALGPEFGG AVGLCFYLGT TF AAAMYIL GAIEIFLVYI VPRAAIFHSD DALKESAAML NNMRVYGTAF LVLMVLVVFI GVRYVNKFAS LFLACVIVSI LAI YAGAIK SSFAPPHFPV CMLGNRTLSS RHIDVCSKTK EINNMTVPSK LWGFFCNSSQ FFNATCDEYF VHNNVTSIQG IPGL ASGII TENLWSNYLP KGEIIEKPSA KSSDVLGSLN HEYVLVDITT SFTLLVGIFF PSVTGIMAGS NRSGDLKDAQ KSIPI GTIL AILTTSFVYL SNVVLFGACI EGVVLRDKFG DAVKGNLVVG TLSWPSPWVI VIGSFFSTCG AGLQSLTGAP RLLQAI AKD NIIPFLRVFG HSKANGEPTW ALLLTAAIAE LGILIASLDL VAPILSMFFL MCYLFVNLAC ALQTLLRTPN WRPRFRY YH WALSFMGMSI CLALMFISSW YYAIVAMVIA GMIYKYIEYQ GAEKEWGDGI RGLSLSAARF ALLRLEEGPP HTKNWRPQ L LVLLKLDEDL HVKHPRLLTF ASQLKAGKGL TIVGSVIVGN FLENYGEALA AEQTIKHLME AEKVKGFCQL VVAAKLREG ISHLIQSCGL GGMKHNTVVM GWPNGWRQSE DARAWKTFIG TVRVTTAAHL ALLVAKNISF FPSNVEQFSE GNIDVWWIVH DGGMLMLLP FLLKQHKVWR KCSIRIFTVA QLEDNSIQMK KDLATFLYHL RIEAEVEVVE MHDSDISAYT YERTLMMEQR S QMLRHMRL SKTERDREAQ LVKDRNSMLR LTSIGSDEDE ETETYQEKVH MTWTKDKYMA SRGQKAKSME GFQDLLNMRP DQ SNVRRMH TAVKLNEVIV NKSHEAKLVL LNMPGPPRNP EGDENYMEFL EVLTEGLERV LLVRGGGSEV ITIYS

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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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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #6: 2-[[(2~{R})-2-butyl-6,7-bis(chloranyl)-2-cyclopentyl-1-oxidanylid...

MacromoleculeName: 2-[[(2~{R})-2-butyl-6,7-bis(chloranyl)-2-cyclopentyl-1-oxidanylidene-3~{H}-inden-5-yl]oxy]ethanoic acid
type: ligand / ID: 6 / Number of copies: 2 / Formula: EZC
Molecular weightTheoretical: 399.308 Da
Chemical component information

ChemComp-EZC:
2-[[(2~{R})-2-butyl-6,7-bis(chloranyl)-2-cyclopentyl-1-oxidanylidene-3~{H}-inden-5-yl]oxy]ethanoic acid

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 40 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 364959

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