+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0472 | |||||||||
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Title | Structure of the TM domain | |||||||||
Map data | Membrane protein | |||||||||
Sample |
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Function / homology | Function and homology information swim bladder inflation / Cation-coupled Chloride cotransporters / chloride:monoatomic cation symporter activity / sodium:potassium:chloride symporter activity / sodium ion homeostasis / ear development / ammonium transmembrane transport / chloride ion homeostasis / ammonium channel activity / potassium ion homeostasis ...swim bladder inflation / Cation-coupled Chloride cotransporters / chloride:monoatomic cation symporter activity / sodium:potassium:chloride symporter activity / sodium ion homeostasis / ear development / ammonium transmembrane transport / chloride ion homeostasis / ammonium channel activity / potassium ion homeostasis / cell volume homeostasis / inner ear morphogenesis / potassium ion import across plasma membrane / sodium ion transmembrane transport / chloride transmembrane transport / basolateral plasma membrane / apical plasma membrane / identical protein binding Similarity search - Function | |||||||||
Biological species | Danio rerio (zebrafish) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Feng L / Liao MF / Orlando B / Zhang JR | |||||||||
Citation | Journal: Nature / Year: 2019 Title: Structure and mechanism of the cation-chloride cotransporter NKCC1. Authors: Thomas A Chew / Benjamin J Orlando / Jinru Zhang / Naomi R Latorraca / Amy Wang / Scott A Hollingsworth / Dong-Hua Chen / Ron O Dror / Maofu Liao / Liang Feng / Abstract: Cation-chloride cotransporters (CCCs) mediate the electroneutral transport of chloride, potassium and/or sodium across the membrane. They have critical roles in regulating cell volume, controlling ...Cation-chloride cotransporters (CCCs) mediate the electroneutral transport of chloride, potassium and/or sodium across the membrane. They have critical roles in regulating cell volume, controlling ion absorption and secretion across epithelia, and maintaining intracellular chloride homeostasis. These transporters are primary targets for some of the most commonly prescribed drugs. Here we determined the cryo-electron microscopy structure of the Na-K-Cl cotransporter NKCC1, an extensively studied member of the CCC family, from Danio rerio. The structure defines the architecture of this protein family and reveals how cytosolic and transmembrane domains are strategically positioned for communication. Structural analyses, functional characterizations and computational studies reveal the ion-translocation pathway, ion-binding sites and key residues for transport activity. These results provide insights into ion selectivity, coupling and translocation, and establish a framework for understanding the physiological functions of CCCs and interpreting disease-related mutations. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0472.map.gz | 24.9 MB | EMDB map data format | |
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Header (meta data) | emd-0472-v30.xml emd-0472.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0472_fsc.xml | 8 KB | Display | FSC data file |
Images | emd_0472.png | 125.4 KB | ||
Others | emd_0472_additional.map.gz | 19.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0472 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0472 | HTTPS FTP |
-Validation report
Summary document | emd_0472_validation.pdf.gz | 470.2 KB | Display | EMDB validaton report |
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Full document | emd_0472_full_validation.pdf.gz | 469.7 KB | Display | |
Data in XML | emd_0472_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | emd_0472_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0472 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0472 | HTTPS FTP |
-Related structure data
Related structure data | 6npkMC 0470C 0471C 0473C 0474C 0475C 6nphC 6npjC 6nplC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0472.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Membrane protein | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.055 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Membrane protein
File | emd_0472_additional.map | ||||||||||||
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Annotation | Membrane protein | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : co-transporter without N-terminal
Entire | Name: co-transporter without N-terminal |
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Components |
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-Supramolecule #1: co-transporter without N-terminal
Supramolecule | Name: co-transporter without N-terminal / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Danio rerio (zebrafish) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Macromolecule #1: Solute carrier family 12 (sodium/potassium/chloride transporter),...
Macromolecule | Name: Solute carrier family 12 (sodium/potassium/chloride transporter), member 2 type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Danio rerio (zebrafish) |
Molecular weight | Theoretical: 50.618133 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: KFGWIKGVLV RCMLNIWGVM LFIRMTWIVG QAGIAYSCII VIMATVVTTI TGCSTSAIAT NGFVRGGGAY YLISRSLGPE FGGSIGLIF AFANAVAVAM YVVGFAETVV ELLMDSGLLM IDQTNDIRVI GTITVILLLG ISVAGMEWEA KAQIFLLVIL I TAIFNYFI ...String: KFGWIKGVLV RCMLNIWGVM LFIRMTWIVG QAGIAYSCII VIMATVVTTI TGCSTSAIAT NGFVRGGGAY YLISRSLGPE FGGSIGLIF AFANAVAVAM YVVGFAETVV ELLMDSGLLM IDQTNDIRVI GTITVILLLG ISVAGMEWEA KAQIFLLVIL I TAIFNYFI GSFIAVDSKK KFGFFSYDAG ILAENFGPDF RGQTFFSVFS IFFPAATGIL AGANISGDLA DPQMAIPKGT LL AILITGL VYVGVAISAG ACIVRDATGI ESNFTLISNC TDAACKYGYD FSSCRPTVEG EVSSCKFGLH NDFQVMSVVS GFS PLISAG IFSATLSSAL ASLVSAPKVF QALCKDNIYP GIAIFGKGYG KNNEPLRGYF LTFGIALAFI LIAELNVIAP IISN FFLAS YALINFSVFH ASLANSPGWR PSFKYYNMWA SLAGAILCCV VMFIINWWAA LLTNVIVLSL YIYVSYK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 7.9 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 96 % / Chamber temperature: 293 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 53.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |