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- EMDB-24813: Cryo-EM structure of Human NKCC1 K289NA492EL671C -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-24813
TitleCryo-EM structure of Human NKCC1 K289NA492EL671C
Map data
Sample
  • Complex: Human NKCC1 K289NA492EL671C
    • Protein or peptide: Solute carrier family 12 member 2
Keywordsion transport / TRANSPORT PROTEIN
Function / homology
Function and homology information


positive regulation of cell volume / positive regulation of aspartate secretion / transepithelial ammonium transport / regulation of matrix metallopeptidase secretion / cell body membrane / metal ion transmembrane transporter activity / inorganic anion import across plasma membrane / inorganic cation import across plasma membrane / chloride:monoatomic cation symporter activity / sodium:potassium:chloride symporter activity ...positive regulation of cell volume / positive regulation of aspartate secretion / transepithelial ammonium transport / regulation of matrix metallopeptidase secretion / cell body membrane / metal ion transmembrane transporter activity / inorganic anion import across plasma membrane / inorganic cation import across plasma membrane / chloride:monoatomic cation symporter activity / sodium:potassium:chloride symporter activity / transepithelial chloride transport / potassium ion transmembrane transporter activity / Cation-coupled Chloride cotransporters / intracellular chloride ion homeostasis / negative regulation of vascular wound healing / ammonium transmembrane transport / sodium ion homeostasis / chloride ion homeostasis / ammonium channel activity / cell projection membrane / cellular response to potassium ion / T cell chemotaxis / cellular response to chemokine / intracellular potassium ion homeostasis / potassium ion homeostasis / intracellular sodium ion homeostasis / sodium ion import across plasma membrane / hyperosmotic response / cell volume homeostasis / gamma-aminobutyric acid signaling pathway / regulation of spontaneous synaptic transmission / maintenance of blood-brain barrier / potassium ion import across plasma membrane / lateral plasma membrane / transport across blood-brain barrier / monoatomic ion transport / chloride transmembrane transport / sodium ion transmembrane transport / cytoplasmic vesicle membrane / basal plasma membrane / cell projection / cell periphery / Hsp90 protein binding / extracellular vesicle / protein-folding chaperone binding / cell body / basolateral plasma membrane / neuron projection / apical plasma membrane / neuronal cell body / protein kinase binding / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Solute carrier family 12 member 1/2 / Solute carrier family 12 member 2 / Amino acid permease, N-terminal / Amino acid permease N-terminal / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhao YX / Cao EH
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for inhibition of the Cation-chloride cotransporter NKCC1 by the diuretic drug bumetanide
Authors: Zhao Y / Roy K / Vidossich P / Cancedda L / De Vivo M / Forbush B / Cao E
History
DepositionSep 2, 2021-
Header (metadata) releaseMay 25, 2022-
Map releaseMay 25, 2022-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24813.png

Downloads & links

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Map

FileDownload / File: emd_24813.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-5.7752886 - 7.275261
Average (Standard dev.)0.009940634 (±0.14999557)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_24813_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human NKCC1 K289NA492EL671C

EntireName: Human NKCC1 K289NA492EL671C
Components
  • Complex: Human NKCC1 K289NA492EL671C
    • Protein or peptide: Solute carrier family 12 member 2

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Supramolecule #1: Human NKCC1 K289NA492EL671C

SupramoleculeName: Human NKCC1 K289NA492EL671C / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 12 member 2

MacromoleculeName: Solute carrier family 12 member 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 131.888641 KDa
Recombinant expressionOrganism: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others)
SequenceString: GAMGSEPRPT APSSGAPGLA GVGETPSAAA LAAARVELPG TAVPSVPEDA APASRDGGGV RDEGPAAAGD GLGRPLGPTP SQSRFQVDL VSENAGRAAA AAAAAAAAAA AAGAGAGAKQ TPADGEASGE SEPAKGSEEA KGRFRVNFVD PAASSSAEDS L SDAAGVGV ...String:
GAMGSEPRPT APSSGAPGLA GVGETPSAAA LAAARVELPG TAVPSVPEDA APASRDGGGV RDEGPAAAGD GLGRPLGPTP SQSRFQVDL VSENAGRAAA AAAAAAAAAA AAGAGAGAKQ TPADGEASGE SEPAKGSEEA KGRFRVNFVD PAASSSAEDS L SDAAGVGV DGPNVSFQNG GDTVLSEGSS LHSGGGGGSG HHQHYYYDTH TNTYYLRTFG HNTMDAVPRI DHYRHTAAQL GE KLLRPSL AELHDELEKE PFEDGFANGE ESTPTRDAVV TYTAESKGVV KFGWINGVLV RCMLNIWGVM LFIRLSWIVG QAG IGLSVL VIMMATVVTT ITGLSTSAIA TNGFVRGGGA YYLISRSLGP EFGGAIGLIF AFANAVAVAM YVVGFAETVV ELLK EHSIL MIDEINDIRI IGAITVVILL GISVAGMEWE AKAQIVLLVI LLLAIGDFVI GTFIPLESKK PKGFFGYKSE IFNEN FGPD FREEETFFSV FEIFFPAATG ILAGANISGD LADPQSALPK GTLLAILITT LVYVGIAVSV GSCVVRDATG NVNDTI VTE LTNCTSAACK LNFDFSSCES SPCSYGLMNN FQVMSMVSGF TPLISAGIFS ATLSSALASL VSAPKIFQAL CKDNIYP AF QMFAKGYGKN NEPLRGYILT FLIALGFILI AECNVIAPII SNFFLASYAL INFSVFHASL AKSPGWRPAF KYYNMWIS L LGAILCCIVM FVINWWAALL TYVIVLGLYI YVTYKKPDVN WGSSTQALTY LNALQHSIRL SGVEDHVKNF RPQCLVMTG APNSRPALLH LVHDFTKNVG LMICGHVHMG PRRQAMKEMS IDQAKYQRWL IKNKMKAFYA PVHADDLREG AQYLMQAAGL GRMKPNTLV LGFKKDWLQA DMRDVDMYIN LFHDAFDIQY GVVVIRLKEG LDISHLQGQE ELLSSQEKSP GTKDVVVSVE Y SKKSDLDT SKPLSEKPIT HKVEEEDGKT ATQPLLKKES KGPIVPLNVA DQKLLEASTQ FQKKQGKNTI DVWWLFDDGG LT LLIPYLL TTKKKWKDCK IRVFIGGKIN RIDHDRRAMA TLLSKFRIDF SDIMVLGDIN TKPKKENIIA FEEIIEPYRL HED DKEQDI ADKMKEDEPW RITDNELELY KTKTYRQIRL NELLKEHSST ANIIVMSLPV ARKGAVSSAL YMAWLEALSK DLPP ILLVR GNHQSVLTFY S

UniProtKB: Solute carrier family 12 member 2

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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 (6k x 4k) / Average electron dose: 1.175 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Number images used: 536763
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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