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- EMDB-30061: cryo_EM map of KCC2 -

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Basic information

Entry
Database: EMDB / ID: EMD-30061
Titlecryo_EM map of KCC2
Map datacryo_EM map of KCC2
Sample
  • Complex: KCC2
    • Protein or peptide: Solute carrier family 12 member 5
  • Ligand: POTASSIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsKCC2 / MEMBRANE PROTEIN
Function / homology
Function and homology information


thermosensory behavior / intracellular pH reduction / potassium:chloride symporter activity / Cation-coupled Chloride cotransporters / hypotonic response / intracellular chloride ion homeostasis / ammonium channel activity / chloride ion homeostasis / dendritic spine development / potassium ion homeostasis ...thermosensory behavior / intracellular pH reduction / potassium:chloride symporter activity / Cation-coupled Chloride cotransporters / hypotonic response / intracellular chloride 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 / 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 / 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 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsChi XM / Li XR
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-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6m23
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30061.png

Downloads & links

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Map

FileDownload / File: emd_30061.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo_EM map of KCC2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 320 pix.
= 347.84 Å		1.09 Å/pix.
x 320 pix.
= 347.84 Å		1.09 Å/pix.
x 320 pix.
= 347.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.018
Minimum - Maximum-0.033730425 - 0.07505515
Average (Standard dev.)0.000038557864 (±0.0020025326)
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-0.0340.0750.000

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Supplemental data

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Sample components

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Entire : KCC2

EntireName: KCC2
Components
  • Complex: KCC2
    • Protein or peptide: Solute carrier family 12 member 5
  • Ligand: POTASSIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: KCC2

SupramoleculeName: KCC2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: Homo sapiens (human)
Molecular weightTheoretical: 125.295617 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADYKDDDDK SGRMLNNLTD CEDGDGGANP GDGNPKESSP FINSTDTEKG KEYDGKNMAL FEEEMDTSPM VSSLLSGLAN YTNLPQGSR EHEEAENNEG GKKKPVQAPR MGTFMGVYLP CLQNIFGVIL FLRLTWVVGI AGIMESFCMV FICCSCTMLT A ISMSAIAT ...String:
MADYKDDDDK SGRMLNNLTD CEDGDGGANP GDGNPKESSP FINSTDTEKG KEYDGKNMAL FEEEMDTSPM VSSLLSGLAN YTNLPQGSR EHEEAENNEG GKKKPVQAPR MGTFMGVYLP CLQNIFGVIL FLRLTWVVGI AGIMESFCMV FICCSCTMLT A ISMSAIAT NGVVPAGGSY YMISRSLGPE FGGAVGLCFY LGTTFAGAMY ILGTIEILLA YLFPAMAIFK AEDASGEAAA ML NNMRVYG TCVLTCMATV VFVGVKYVNK FALVFLGCVI LSILAIYAGV IKSAFDPPNF PICLLGNRTL SRHGFDVCAK LAW EGNETV TTRLWGLFCS SRFLNATCDE YFTRNNVTEI QGIPGAASGL IKENLWSSYL TKGVIVERSG MTSVGLADGT PIDM DHPYV FSDMTSYFTL LVGIYFPSVT GIMAGSNRSG DLRDAQKSIP TGTILAIATT SAVYISSVVL FGACIEGVVL RDKFG EAVN GNLVVGTLAW PSPWVIVIGS FFSTCGAGLQ SLTGAPRLLQ AISRDGIVPF LQVFGHGKAN GEPTWALLLT ACICEI GIL IASLDEVAPI LSMFFLMCYM FVNLACAVQT LLRTPNWRPR FRYYHWTLSF LGMSLCLALM FICSWYYALV AMLIAGL IY KYIEYRGAEK EWGDGIRGLS LSAARYALLR LEEGPPHTKN WRPQLLVLVR VDQDQNVVHP QLLSLTSQLK AGKGLTIV G SVLEGTFLEN HPQAQRAEES IRRLMEAEKV KGFCQVVISS NLRDGVSHLI QSGGLGGLQH NTVLVGWPRN WRQKEDHQT WRNFIELVRE TTAGHLALLV TKNVSMFPGN PERFSEGSID VWWIVHDGGM LMLLPFLLRH HKVWRKCKMR IFTVAQMDDN SIQMKKDLT TFLYHLRITA EVEVVEMHES DISAYTYEK(TPO) LVMEQRSQIL KQMHLTKNER EREIQSITDE SRGSIRR KN PANTRLRLNV PEETAGDSEE KPEEEVQLIH DQSAPSCPSS SPSPGEEPEG EGETDPEKVH L(TPO)WTKDKSVA EKNK GPSPV SSEGIKDFFS MKPEWENLNQ SNVRRMHTAV RLNEVIVKKS RDAKLVLLNM PGPPRNRNGD ENYMEFLEVL TEHLD RVML VRGGGREVIT IYS

UniProtKB: Solute carrier family 12 member 5

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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: 2 / 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: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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
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

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 186236
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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