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Yorodumi- EMDB-24807: Cryo-EM structure of human NKCC1 K289NA492EL671C bound with bumetanide -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24807 | |||||||||
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Title | Cryo-EM structure of human NKCC1 K289NA492EL671C 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: 2.9 Å | |||||||||
Authors | Zhao YX / Cao EH | |||||||||
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_24807.map.gz | 59.6 MB | EMDB map data format | |
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Header (meta data) | emd-24807-v30.xml emd-24807.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
Images | emd_24807.png | 37 KB | ||
Others | emd_24807_additional_1.map.gz | 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24807 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24807 | HTTPS FTP |
-Validation report
Summary document | emd_24807_validation.pdf.gz | 462.6 KB | Display | EMDB validaton report |
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Full document | emd_24807_full_validation.pdf.gz | 462.2 KB | Display | |
Data in XML | emd_24807_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | emd_24807_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24807 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24807 | HTTPS FTP |
-Related structure data
Related structure data | 7s1xMC 7s1yC 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-11049 (Title: Cryo-EM structure of human NKCC1 K289NA492EL671C bound with bumetanide Data size: 1.8 TB Data #1: Cryo-EM structure of human NKCC1 K289NA492EL671C bound with bumetanide [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_24807.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_24807_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human NKCC1 K289NA492EL671C bound with bumetanide
Entire | Name: human NKCC1 K289NA492EL671C bound with bumetanide |
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Components |
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-Supramolecule #1: human NKCC1 K289NA492EL671C bound with bumetanide
Supramolecule | Name: human NKCC1 K289NA492EL671C 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) |
Molecular weight | Theoretical: 263.34 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: 131.888641 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 LHSGGGGGSG HHQHYYYDTH TNTYYLRTFG HNTMDAVPRI DHYRHTAAQL GE KLLRPSL AELHDELEKE PFEDGFANGE ESTPTRDAVV TYTAESKGVV KFGWINGVLV RCMLNIWGVM LFIRLSWIVG QAG IGLSVL VIMMATVVTT ITGLSTSAIA TNGFVRGGGA YYLISRSLGP EFGGAIGLIF AFANAVAVAM YVVGFAETVV ELLK EHSIL MIDEINDIRI IGAITVVILL GISVAGMEWE AKAQIVLLVI LLLAIGDFVI GTFIPLESKK PKGFFGYKSE IFNEN FGPD FREEETFFSV FEIFFPAATG ILAGANISGD LADPQSAIPK GTLLAILITT LVYVGIAVSV GSCVVRDATG NVNDTI VTE LTNCTSAACK LNFDFSSCES SPCSYGLMNN FQVMSMVSGF TPLISAGIFS ATLSSALASL VSAPKIFQAL CKDNIYP AF QMFAKGYGKN NEPLRGYILT FLIALGFILI AECNVIAPII SNFFLASYAL INFSVFHASL AKSPGWRPAF KYYNMWIS L LGAILCCIVM FVINWWAALL TYVIVLGLYI YVTYKKPDVN WGSSTQALTY LNALQHSIRL SGVEDHVKNF RPQCLVMTG APNSRPALLH LVHDFTKNVG LMICGHVHMG PRRQAMKEMS IDQAKYQRWL IKNKMKAFYA PVHADDLREG AQYLMQAAGL GRMKPNTLV LGFKKDWLQA DMRDVDMYIN LFHDAFDIQY GVVVIRLKEG LDISHLQGQE ELLSSQEKSP GTKDVVVSVE Y SKKSDLDT SKPLSEKPIT HKVEEEDGKT ATQPLLKKES KGPIVPLNVA DQKLLEASTQ FQKKQGKNTI DVWWLFDDGG LT LLIPYLL TTKKKWKDCK IRVFIGGKIN RIDHDRRAMA TLLSKFRIDF SDIMVLGDIN TKPKKENIIA FEEIIEPYRL HED DKEQDI ADKMKEDEPW RITDNELELY KTKTYRQIRL NELLKEHSST ANIIVMSLPV ARKGAVSSAL YMAWLEALSK DLPP ILLVR GNHQSVLTFY S |
-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: 2 / 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 |
-Macromolecule #4: CHLORIDE ION
Macromolecule | Name: CHLORIDE ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CL |
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Molecular weight | Theoretical: 35.453 Da |
-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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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
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 |