+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24141 | |||||||||
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Title | CryoEM structure of human NKCC1 state Fu-I | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Sodium / potassium / chloride / co-transporter / ions / human / CTD / TMD / full-length / MEMBRANE PROTEIN / furosemide / diuretic / loop diuretic | |||||||||
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 / inorganic anion import across plasma membrane / inorganic cation import across plasma membrane / metal ion transmembrane transporter activity / 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 / inorganic anion import across plasma membrane / inorganic cation import across plasma membrane / metal ion transmembrane transporter activity / 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 / sodium ion homeostasis / negative regulation of vascular wound healing / ammonium transmembrane transport / chloride ion homeostasis / ammonium channel activity / cellular response to potassium ion / cell projection membrane / intracellular potassium ion homeostasis / cellular response to chemokine / T cell chemotaxis / sodium ion import across plasma membrane / potassium ion homeostasis / intracellular sodium ion homeostasis / 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 / transport across blood-brain barrier / lateral plasma membrane / sodium ion transmembrane transport / monoatomic ion transport / chloride transmembrane transport / basal plasma membrane / cell projection / cell periphery / Hsp90 protein binding / cytoplasmic vesicle membrane / 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 | |||||||||
Biological species | Homo sapiens (human) / human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.33 Å | |||||||||
Authors | Moseng MA | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Sci Adv / Year: 2022 Title: Inhibition mechanism of NKCC1 involves the carboxyl terminus and long-range conformational coupling. Authors: Mitchell A Moseng / Chih-Chia Su / Kerri Rios / Meng Cui / Meinan Lyu / Przemyslaw Glaza / Philip A Klenotic / Eric Delpire / Edward W Yu / Abstract: The Na-K-2Cl cotransporter-1 (NKCC1) is an electroneutral Na-dependent transporter responsible for simultaneously translocating Na, K, and Cl ions into cells. In human tissue, NKCC1 plays a critical ...The Na-K-2Cl cotransporter-1 (NKCC1) is an electroneutral Na-dependent transporter responsible for simultaneously translocating Na, K, and Cl ions into cells. In human tissue, NKCC1 plays a critical role in regulating cytoplasmic volume, fluid intake, chloride homeostasis, and cell polarity. Here, we report four structures of human NKCC1 (hNKCC1), both in the absence and presence of loop diuretic (bumetanide or furosemide), using single-particle cryo-electron microscopy. These structures allow us to directly observe various novel conformations of the hNKCC1 dimer. They also reveal two drug-binding sites located at the transmembrane and cytosolic carboxyl-terminal domains, respectively. Together, our findings enable us to delineate an inhibition mechanism that involves a coupled movement between the cytosolic and transmembrane domains of hNKCC1. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_24141.map.gz | 230.1 MB | EMDB map data format | |
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Header (meta data) | emd-24141-v30.xml emd-24141.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24141_fsc.xml | 13.2 KB | Display | FSC data file |
Images | emd_24141.png | 134.2 KB | ||
Masks | emd_24141_msk_1.map | 244.1 MB | Mask map | |
Others | emd_24141_half_map_1.map.gz emd_24141_half_map_2.map.gz | 226.6 MB 226.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24141 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24141 | HTTPS FTP |
-Validation report
Summary document | emd_24141_validation.pdf.gz | 1002.7 KB | Display | EMDB validaton report |
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Full document | emd_24141_full_validation.pdf.gz | 1002.3 KB | Display | |
Data in XML | emd_24141_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | emd_24141_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24141 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24141 | HTTPS FTP |
-Related structure data
Related structure data | 7n3nMC 7mxoC 7sflC 7smpC 8steC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_24141.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_24141_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_24141_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_24141_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human NKCC1 in a detergent micelle with furosemide
Entire | Name: human NKCC1 in a detergent micelle with furosemide |
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Components |
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-Supramolecule #1: human NKCC1 in a detergent micelle with furosemide
Supramolecule | Name: human NKCC1 in a detergent micelle with furosemide / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 131 MDa |
-Macromolecule #1: Solute carrier family 12 member 2
Macromolecule | Name: Solute carrier family 12 member 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: human (human) |
Molecular weight | Theoretical: 131.583422 KDa |
Sequence | String: MEPRPTAPSS GAPGLAGVGE TPSAAALAAA RVELPGTAVP SVPEDAAPAS RDGGGVRDEG PAAAGDGLGR PLGPTPSQSR FQVDLVSEN AGRAAAAAAA AAAAAAAAGA GAGAKQTPAD GEASGESEPA KGSEEAKGRF RVNFVDPAAS SSAEDSLSDA A GVGVDGPN ...String: MEPRPTAPSS GAPGLAGVGE TPSAAALAAA RVELPGTAVP SVPEDAAPAS RDGGGVRDEG PAAAGDGLGR PLGPTPSQSR FQVDLVSEN AGRAAAAAAA AAAAAAAAGA GAGAKQTPAD GEASGESEPA KGSEEAKGRF RVNFVDPAAS SSAEDSLSDA A GVGVDGPN VSFQNGGDTV LSEGSSLHSG GGGGSGHHQH YYYDTHTNTY YLRTFGHNTM DAVPRIDHYR HTAAQLGEKL LR PSLAELH DELEKEPFED GFANGEESTP TRDAVVTYTA ESKGVVKFGW IKGVLVRCML NIWGVMLFIR LSWIVGQAGI GLS VLVIMM ATVVTTITGL STSAIATNGF VRGGGAYYLI SRSLGPEFGG AIGLIFAFAN AVAVAMYVVG FAETVVELLK EHSI LMIDE INDIRIIGAI TVVILLGISV AGMEWEAKAQ IVLLVILLLA IGDFVIGTFI PLESKKPKGF FGYKSEIFNE NFGPD FREE ETFFSVFAIF FPAATGILAG ANISGDLADP QSAIPKGTLL AILITTLVYV GIAVSVGSCV VRDATGNVND TIVTEL TNC TSAACKLNFD FSSCESSPCS YGLMNNFQVM SMVSGFTPLI SAGIFSATLS SALASLVSAP KIFQALCKDN IYPAFQM FA KGYGKNNEPL RGYILTFLIA LGFILIAELN VIAPIISNFF LASYALINFS VFHASLAKSP GWRPAFKYYN MWISLLGA I LCCIVMFVIN WWAALLTYVI VLGLYIYVTY KKPDVNWGSS TQALTYLNAL QHSIRLSGVE DHVKNFRPQC LVMTGAPNS RPALLHLVHD FTKNVGLMIC GHVHMGPRRQ AMKEMSIDQA KYQRWLIKNK MKAFYAPVHA DDLREGAQYL MQAAGLGRMK PNTLVLGFK KDWLQADMRD VDMYINLFHD AFDIQYGVVV IRLKEGLDIS HLQGQEELLS SQEKSPGTKD VVVSVEYSKK S DLDTSKPL SEKPITHKVE EEDGKTATQP LLKKESKGPI VPLNVADQKL LEASTQFQKK QGKNTIDVWW LFDDGGLTLL IP YLLTTKK KWKDCKIRVF IGGKINRIDH DRRAMATLLS KFRIDFSDIM VLGDINTKPK KENIIAFEEI IEPYRLHEDD KEQ DIADKM KEDEPWRITD NELELYKTKT YRQIRLNELL KEHSSTANII VMSLPVARKG AVSSALYMAW LEALSKDLPP ILLV RGNHQ SVLTFYS |
-Macromolecule #2: 5-(AMINOSULFONYL)-4-CHLORO-2-[(2-FURYLMETHYL)AMINO]BENZOIC ACID
Macromolecule | Name: 5-(AMINOSULFONYL)-4-CHLORO-2-[(2-FURYLMETHYL)AMINO]BENZOIC ACID type: ligand / ID: 2 / Number of copies: 2 / Formula: FUN |
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Molecular weight | Theoretical: 330.744 Da |
Chemical component information | ChemComp-FUN: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |