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- PDB-6m23: Overall structure of KCC2 -

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Basic information

Entry
Database: PDB / ID: 6m23
TitleOverall structure of KCC2
ComponentsSolute carrier family 12 member 5
KeywordsMEMBRANE PROTEIN / KCC2
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 / intracellular monoatomic ion homeostasis / chloride ion homeostasis / ammonium transmembrane transporter activity / dendritic spine development ...thermosensory behavior / intracellular pH reduction / potassium:chloride symporter activity / Cation-coupled Chloride cotransporters / hypotonic response / intracellular chloride ion homeostasis / intracellular monoatomic ion homeostasis / chloride ion homeostasis / ammonium transmembrane transporter activity / dendritic spine development / potassium ion homeostasis / cell volume homeostasis / chloride transmembrane transporter activity / potassium ion import across plasma membrane / plasma membrane => GO:0005886 / monoatomic ion transport / chloride transmembrane transport / dendrite membrane / learning / cell periphery / multicellular organism growth / perikaryon / chemical synaptic transmission / membrane => GO:0016020 / 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 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 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsChi, X.M. / Li, X.R. / Chen, Y. / Zhang, Y.Y. / Su, Q. / Zhou, Q.
Funding support China, 3items
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, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
A: Solute carrier family 12 member 5
B: Solute carrier family 12 member 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,72914
Polymers250,5912
Non-polymers3,13812
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area10180 Å2
ΔGint-22 kcal/mol
Surface area84820 Å2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Solute carrier family 12 member 5 / Electroneutral potassium-chloride cotransporter 2 / K-Cl cotransporter 2 / hKCC2 / Neuronal K-Cl cotransporter


Mass: 125295.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCC2 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9H2X9

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Sugars , 2 types, 8 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 6 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: KCC2 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293F
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: RELION / Version: 3.0.6 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 186236 / Symmetry type: POINT

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