+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24074 | |||||||||
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Title | CryoEM structure of human NKCC1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Sodium / potassium / chloride / co-transporter / ions / human / CTD / TMD / full-length / MEMBRANE 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 / 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) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.47 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_24074.map.gz | 168.1 MB | EMDB map data format | |
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Header (meta data) | emd-24074-v30.xml emd-24074.xml | 14.9 KB 14.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24074_fsc.xml | 11.9 KB | Display | FSC data file |
Images | emd_24074.png | 149.5 KB | ||
Masks | emd_24074_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-24074.cif.gz | 5.7 KB | ||
Others | emd_24074_half_map_1.map.gz emd_24074_half_map_2.map.gz | 165.1 MB 165.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24074 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24074 | HTTPS FTP |
-Validation report
Summary document | emd_24074_validation.pdf.gz | 891 KB | Display | EMDB validaton report |
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Full document | emd_24074_full_validation.pdf.gz | 890.6 KB | Display | |
Data in XML | emd_24074_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | emd_24074_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24074 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24074 | HTTPS FTP |
-Related structure data
Related structure data | 7mxoMC 7n3nC 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_24074.map.gz / Format: CCP4 / Size: 178 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: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_24074_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_24074_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_24074_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Full-length human NKCC1 with NaCl and KCl
Entire | Name: Full-length human NKCC1 with NaCl and KCl |
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Components |
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-Supramolecule #1: Full-length human NKCC1 with NaCl and KCl
Supramolecule | Name: Full-length human NKCC1 with NaCl and KCl / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 131 KDa |
-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: Homo sapiens (human) |
Molecular weight | Theoretical: 102.518414 KDa |
Sequence | String: KFGWIKGVLV RCMLNIWGVM LFIRLSWIVG QAGIGLSVLV IMMATVVTTI TGLSTSAIAT NGFVRGGGAY YLISRSLGPE FGGAIGLIF AFANAVAVAM YVVGFAETVV ELLKEHSILM IDEINDIRII GAITVVILLG ISVAGMEWEA KAQIVLLVIL L LAIGDFVI ...String: KFGWIKGVLV RCMLNIWGVM LFIRLSWIVG QAGIGLSVLV IMMATVVTTI TGLSTSAIAT NGFVRGGGAY YLISRSLGPE FGGAIGLIF AFANAVAVAM YVVGFAETVV ELLKEHSILM IDEINDIRII GAITVVILLG ISVAGMEWEA KAQIVLLVIL L LAIGDFVI GTFIPLESKK PKGFFGYKSE IFNENFGPDF REEETFFSVF AIFFPAATGI LAGANISGDL ADPQSAIPKG TL LAILITT LVYVGIAVSV GSCVVRDATG NVNDTIVTEL TNCTSAACKL NFDFSSCESS PCSYGLMNNF QVMSMVSGFT PLI SAGIFS ATLSSALASL VSAPKIFQAL CKDNIYPAFQ MFAKGYGKNN EPLRGYILTF LIALGFILIA ELNVIAPIIS NFFL ASYAL INFSVFHASL AKSPGWRPAF KYYNMWISLL GAILCCIVMF VINWWAALLT YVIVLGLYIY VTYKKPDVNW GSSTQ ALTY LNALQHSIRL SGVEDHVKNF RPQCLVMTGA PNSRPALLHL VHDFTKNVGL MICGHVHMGP RRQAMKEMSI DQAKYQ RWL IKNKMKAFYA PVHADDLREG AQYLMQAAGL GRMKPNTLVL GFKKDWLQAD MRDVDMYINL FHDAFDIQYG VVVIRLK EG LDISHLQGQE ELLSSQEKSP GTKDVVVSVE YSKKSDLDTS KPLSEKPITH KVEEEDGKTA TQPLLKKESK GPIVPLNV A DQKLLEASTQ FQQKQGKNTI DVWWLFDDGG LTLLIPYLLT TKKKWKDCKI RVFIGGKINR IDHDRRAMAT LLSKFRIDF SDIMVLGDIN TKPKKENIIA FEEIIEPYRL HEDDKEQDIA DKMKEDEPWR ITDNELELYK TKTYRQIRLN ELLKEHSSTA NIIVMSLPV ARKGAVSSAL YMAWLEALSK DLPPILLVRG NHQS UniProtKB: Solute carrier family 12 member 2 |
-Macromolecule #2: CHLORIDE ION
Macromolecule | Name: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: CL |
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Molecular weight | Theoretical: 35.453 Da |
-Macromolecule #3: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-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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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 |
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 |