+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25204 | |||||||||
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Title | CryoEM structure of NKCC1 Bu-I | |||||||||
Map data | Cryo-EM structure of NKCC1 Bu-I | |||||||||
Sample |
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Keywords | cotransporter / dimer / ion / MEMBRANE PROTEIN / 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 / inorganic anion import across plasma membrane / inorganic cation import across plasma membrane / chloride:monoatomic cation symporter activity / sodium:potassium:chloride symporter activity / metal ion transmembrane transporter 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 / chloride:monoatomic cation symporter activity / sodium:potassium:chloride symporter activity / metal ion transmembrane transporter activity / transepithelial chloride transport / potassium ion transmembrane transporter activity / Cation-coupled Chloride cotransporters / ammonium transmembrane transport / sodium ion homeostasis / intracellular chloride ion homeostasis / negative regulation of vascular wound healing / chloride ion homeostasis / cellular response to potassium ion / ammonium channel activity / intracellular potassium ion homeostasis / cell projection membrane / intracellular sodium ion homeostasis / sodium ion import across plasma membrane / potassium ion homeostasis / cellular response to chemokine / T cell chemotaxis / hyperosmotic response / gamma-aminobutyric acid signaling pathway / cell volume homeostasis / regulation of spontaneous synaptic transmission / maintenance of blood-brain barrier / potassium ion import across plasma membrane / transport across blood-brain barrier / sodium ion transmembrane transport / lateral plasma membrane / monoatomic ion transport / chloride transmembrane transport / basal plasma membrane / cell projection / cell periphery / Hsp90 protein binding / cytoplasmic vesicle membrane / extracellular vesicle / cell body / protein-folding chaperone binding / 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: 3.28 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_25204.map.gz | 230 MB | EMDB map data format | |
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Header (meta data) | emd-25204-v30.xml emd-25204.xml | 14.9 KB 14.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25204_fsc.xml | 13.2 KB | Display | FSC data file |
Images | emd_25204.png | 149.5 KB | ||
Masks | emd_25204_msk_1.map | 244.1 MB | Mask map | |
Others | emd_25204_half_map_1.map.gz emd_25204_half_map_2.map.gz | 226.6 MB 226.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25204 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25204 | HTTPS FTP |
-Related structure data
Related structure data | 7smpMC 7mxoC 7n3nC 7sflC 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_25204.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM structure of NKCC1 Bu-I | ||||||||||||||||||||
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_25204_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half Map 1
File | emd_25204_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 2
File | emd_25204_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : NKCC1 Bu-I
Entire | Name: NKCC1 Bu-I |
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Components |
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-Supramolecule #1: NKCC1 Bu-I
Supramolecule | Name: NKCC1 Bu-I / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-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: 103.313422 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AVKFGWIKGV LVRCMLNIWG VMLFIRLSWI VGQAGIGLSV LVIMMATVVT TITGLSTSAI ATNGFVRGGG AYYLISRSLG PEFGGAIGL IFAFANAVAV AMYVVGFAET VVELLKEHSI LMIDEINDIR IIGAITVVIL LGISVAGMEW EAKAQIVLLV I LLLAIGDF ...String: AVKFGWIKGV LVRCMLNIWG VMLFIRLSWI VGQAGIGLSV LVIMMATVVT TITGLSTSAI ATNGFVRGGG AYYLISRSLG PEFGGAIGL IFAFANAVAV AMYVVGFAET VVELLKEHSI LMIDEINDIR IIGAITVVIL LGISVAGMEW EAKAQIVLLV I LLLAIGDF VIGTFIPLES KKPKGFFGYK SEIFNENFGP DFREEETFFS VFAIFFPAAT GILAGANISG DLADPQSAIP KG TLLAILI TTLVYVGIAV SVGSCVVRDA TGNVNDTIVT ELTNCTSAAC KLNFDFSSCE SSPCSYGLMN NFQVMSMVSG FTP LISAGI FSATLSSALA SLVSAPKIFQ ALCKDNIYPA FQMFAKGYGK NNEPLRGYIL TFLIALGFIL IAELNVIAPI ISNF FLASY ALINFSVFHA SLAKSPGWRP AFKYYNMWIS LLGAILCCIV MFVINWWAAL LTYVIVLGLY IYVTYKKPDV NWGSS TQAL TYLNALQHSI RLSGVEDHVK NFRPQCLVMT GAPNSRPALL HLVHDFTKNV GLMICGHVHM GPRRQAMKEM SIDQAK YQR WLIKNKMKAF YAPVHADDLR EGAQYLMQAA GLGRMKPNTL VLGFKKDWLQ ADMRDVDMYI NLFHDAFDIQ YGVVVIR LK EGLDISHLQG QEELLSSQEK SPGTKDVVVS VEYSKKSDLD TSKPLSEKPI THKVEEEDGK TATQPLLKKE SKGPIVPL N VADQKLLEAS TQFQKKQGKN TIDVWWLFDD GGLTLLIPYL LTTKKKWKDC KIRVFIGGKI NRIDHDRRAM ATLLSKFRI DFSDIMVLGD INTKPKKENI IAFEEIIEPY RLHEDDKEQD IADKMKEDEP WRITDNELEL YKTKTYRQIR LNELLKEHSS TANIIVMSL PVARKGAVSS ALYMAWLEAL SKDLPPILLV RGNHQSVLTF Y |
-Macromolecule #2: 3-(butylamino)-4-phenoxy-5-sulfamoylbenzoic acid
Macromolecule | Name: 3-(butylamino)-4-phenoxy-5-sulfamoylbenzoic acid / type: ligand / ID: 2 / Number of copies: 3 / Formula: 82U |
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Molecular weight | Theoretical: 364.416 Da |
Chemical component information | ChemComp-82U: |
-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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |