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- EMDB-24812: Cryo-EM structure of human NKCC1 K289NA492E bound with bumetanide -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-24812
TitleCryo-EM structure of human NKCC1 K289NA492E bound with bumetanide
Map data
Sample
  • Complex: hNKCC1 K289NA492E bound with bumetanide
    • Protein or peptide: Solute carrier family 12 member 2
  • Ligand: POTASSIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: 3-(butylamino)-4-phenoxy-5-sulfamoylbenzoic acid
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 / Cation-coupled Chloride cotransporters / potassium ion transmembrane transporter activity / intracellular chloride ion homeostasis / negative regulation of vascular wound healing / ammonium transmembrane transport / sodium ion homeostasis / ammonium channel activity / chloride ion homeostasis / cell projection membrane / cellular response to potassium ion / T cell chemotaxis / cellular response to chemokine / potassium ion homeostasis / intracellular sodium ion homeostasis / hyperosmotic response / sodium ion import across plasma membrane / intracellular potassium ion homeostasis / cell volume homeostasis / regulation of spontaneous synaptic transmission / gamma-aminobutyric acid signaling pathway / maintenance of blood-brain barrier / potassium ion import across plasma membrane / lateral plasma membrane / transport across blood-brain barrier / monoatomic ion transport / sodium ion transmembrane transport / cytoplasmic vesicle membrane / chloride transmembrane transport / basal plasma membrane / cell periphery / cell projection / 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: 3.6 Å
AuthorsZhao YX / Cao E
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-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24812.png

Downloads & links

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Map

FileDownload / File: emd_24812.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-2.3452425 - 3.2074893
Average (Standard dev.)0.008169603 (±0.073862545)
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_24812_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 : hNKCC1 K289NA492E bound with bumetanide

EntireName: hNKCC1 K289NA492E bound with bumetanide
Components
  • Complex: hNKCC1 K289NA492E bound with bumetanide
    • Protein or peptide: Solute carrier family 12 member 2
  • Ligand: POTASSIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: 3-(butylamino)-4-phenoxy-5-sulfamoylbenzoic acid

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Supramolecule #1: hNKCC1 K289NA492E bound with bumetanide

SupramoleculeName: hNKCC1 K289NA492E bound with bumetanide / 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 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: 131.841594 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 LHSGGGGSGH HQHYYYDTHT NTYYLRTFGH NTMDAVPRID HYRHTAAQLG EK LLRPSLA ELHDELEKEP FEDGFANGEE STPTRDAVVT YTAESKGVVK FGWINGVLVR CMLNIWGVML FIRLSWIVGQ AGI GLSVLV IMMATVVTTI TGLSTSAIAT NGFVRGGGAY YLISRSLGPE FGGAIGLIFA FANAVAVAMY VVGFAETVVE LLKE HSILM IDEINDIRII GAITVVILLG ISVAGMEWEA KAQIVLLVIL LLAIGDFVIG TFIPLESKKP KGFFGYKSEI FNENF GPDF REEETFFSVF EIFFPAATGI LAGANISGDL ADPQSALPKG TLLAILITTL VYVGIAVSVG SCVVRDATGN VNDTIV TEL TNCTSAACKL NFDFSSCESS PCSYGLMNNF QVMSMVSGFT PLISAGIFSA TLSSALASLV SAPKIFQALC KDNIYPA FQ MFAKGYGKNN EPLRGYILTF LIALGFILIA ELNVIAPIIS NFFLASYALI NFSVFHASLA KSPGWRPAFK YYNMWISL L GAILCCIVMF VINWWAALLT YVIVLGLYIY VTYKKPDVNW GSSTQALTYL NALQHSIRLS GVEDHVKNFR PQCLVMTGA PNSRPALLHL VHDFTKNVGL MICGHVHMGP RRQAMKEMSI DQAKYQRWLI KNKMKAFYAP VHADDLREGA QYLMQAAGLG RMKPNTLVL GFKKDWLQAD MRDVDMYINL FHDAFDIQYG VVVIRLKEGL DISHLQGQEE LLSSQEKSPG TKDVVVSVEY S KKSDLDTS KPLSEKPITH KVEEEDGKTA TQPLLKKESK GPIVPLNVAD QKLLEASTQF QKKQGKNTID VWWLFDDGGL TL LIPYLLT TKKKWKDCKI RVFIGGKINR IDHDRRAMAT LLSKFRIDFS DIMVLGDINT KPKKENIIAF EEIIEPYRLH EDD KEQDIA DKMKEDEPWR ITDNELELYK TKTYRQIRLN ELLKEHSSTA NIIVMSLPVA RKGAVSSALY MAWLEALSKD LPPI LLVRG NHQSVLTFYS

UniProtKB: Solute carrier family 12 member 2

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #3: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #4: 3-(butylamino)-4-phenoxy-5-sulfamoylbenzoic acid

MacromoleculeName: 3-(butylamino)-4-phenoxy-5-sulfamoylbenzoic acid / type: ligand / ID: 4 / Number of copies: 2 / Formula: 82U
Molecular weightTheoretical: 364.416 Da
Chemical component information

ChemComp-82U:
3-(butylamino)-4-phenoxy-5-sulfamoylbenzoic acid / medication*YM

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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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Number images used: 1033074
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7s1y:
Cryo-EM structure of human NKCC1 K289NA492E bound with bumetanide

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