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Yorodumi- PDB-7s1x: Cryo-EM structure of human NKCC1 K289NA492EL671C bound with bumetanide -
+Open data
-Basic information
Entry | Database: PDB / ID: 7s1x | ||||||
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Title | Cryo-EM structure of human NKCC1 K289NA492EL671C bound with bumetanide | ||||||
Components | Solute carrier family 12 member 2 | ||||||
Keywords | TRANSPORT PROTEIN / cation-chloride cotransporter / ion transport | ||||||
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 / sodium ion homeostasis / intracellular chloride ion homeostasis / negative regulation of vascular wound healing / ammonium transmembrane transport / chloride ion homeostasis / cellular response to potassium ion / cell projection membrane / ammonium channel activity / intracellular potassium ion homeostasis / potassium ion homeostasis / sodium ion import across plasma membrane / T cell chemotaxis / cellular response to chemokine / 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 / basal plasma membrane / chloride transmembrane transport / cell projection / cell periphery / Hsp90 protein binding / cytoplasmic vesicle membrane / extracellular vesicle / protein-folding chaperone binding / basolateral plasma membrane / cell body / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Zhao, Y.X. / Cao, E.H. | ||||||
Funding support | 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7s1x.cif.gz | 306.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s1x.ent.gz | 239.7 KB | Display | PDB format |
PDBx/mmJSON format | 7s1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/7s1x ftp://data.pdbj.org/pub/pdb/validation_reports/s1/7s1x | HTTPS FTP |
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-Related structure data
Related structure data | 24807MC 7s1yC 7s1zC M: map data used to model this data C: citing same article (ref.) |
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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
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 131888.641 Da / Num. of mol.: 2 / Mutation: K289N,A492E,L671C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC12A2, NKCC1 Production host: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others) References: UniProt: P55011 #2: Chemical | #3: Chemical | #4: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: human NKCC1 K289NA492EL671C bound with bumetanide / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.26334 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.175 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18_3845: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 504481 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Num. of particles: 504481 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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