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Yorodumi- EMDB-24812: Cryo-EM structure of human NKCC1 K289NA492E bound with bumetanide -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24812 | |||||||||
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Title | Cryo-EM structure of human NKCC1 K289NA492E bound with bumetanide | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information positive regulation of cell volume / positive regulation of aspartate secretion / transepithelial ammonium transport / regulation of matrix metallopeptidase secretion / metal ion transmembrane transporter activity / 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 ...positive regulation of cell volume / positive regulation of aspartate secretion / transepithelial ammonium transport / regulation of matrix metallopeptidase secretion / metal ion transmembrane transporter activity / 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 / 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 / cell projection membrane / ammonium channel activity / intracellular potassium ion homeostasis / potassium ion homeostasis / T cell chemotaxis / cellular response to chemokine / sodium ion import across plasma membrane / 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: 3.6 Å | |||||||||
Authors | Zhao YX / Cao E | |||||||||
Funding support | 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_24812.map.gz | 59.6 MB | EMDB map data format | |
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Header (meta data) | emd-24812-v30.xml emd-24812.xml | 13.5 KB 13.5 KB | Display Display | EMDB header |
Images | emd_24812.png | 36.3 KB | ||
Others | emd_24812_additional_1.map.gz | 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24812 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24812 | HTTPS FTP |
-Validation report
Summary document | emd_24812_validation.pdf.gz | 425.5 KB | Display | EMDB validaton report |
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Full document | emd_24812_full_validation.pdf.gz | 425.1 KB | Display | |
Data in XML | emd_24812_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | emd_24812_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24812 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24812 | HTTPS FTP |
-Related structure data
Related structure data | 7s1yMC 7s1xC 7s1zC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
EM raw data | EMPIAR-11048 (Title: Cryo-EM structure of human NKCC1 K289NA492E bound with bumetanide Data size: 2.1 TB Data #1: Cryo-EM structure of human NKCC1 K289NA492E bound with bumetanide [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_24812.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_24812_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : hNKCC1 K289NA492E bound with bumetanide
Entire | Name: hNKCC1 K289NA492E bound with bumetanide |
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Components |
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-Supramolecule #1: hNKCC1 K289NA492E bound with bumetanide
Supramolecule | Name: hNKCC1 K289NA492E bound with bumetanide / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others) |
-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: 131.841594 KDa |
Recombinant expression | Organism: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others) |
Sequence | String: 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 |
-Macromolecule #2: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-Macromolecule #3: CHLORIDE ION
Macromolecule | Name: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: CL |
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Molecular weight | Theoretical: 35.453 Da |
-Macromolecule #4: 3-(butylamino)-4-phenoxy-5-sulfamoylbenzoic acid
Macromolecule | Name: 3-(butylamino)-4-phenoxy-5-sulfamoylbenzoic acid / type: ligand / ID: 4 / Number of copies: 2 / Formula: 82U |
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Molecular weight | Theoretical: 364.416 Da |
Chemical component information | ChemComp-82U: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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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: 1.175 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Number images used: 1033074 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7s1y: |