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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0472 | |||||||||
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Title | Structure of the TM domain | |||||||||
![]() | Membrane protein | |||||||||
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Function / homology | ![]() swim bladder inflation / Cation-coupled Chloride cotransporters / salt transmembrane transporter activity / chloride:monoatomic cation symporter activity / sodium:potassium:chloride symporter activity / sodium ion homeostasis / chloride ion homeostasis / ear development / ammonium channel activity / potassium ion homeostasis ...swim bladder inflation / Cation-coupled Chloride cotransporters / salt transmembrane transporter activity / chloride:monoatomic cation symporter activity / sodium:potassium:chloride symporter activity / sodium ion homeostasis / chloride ion homeostasis / ear development / 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 | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Feng L / Liao MF / Orlando B / Zhang JR | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 24.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.8 KB 12.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8 KB | Display | ![]() |
Images | ![]() | 125.4 KB | ||
Others | ![]() | 19.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 470.2 KB | Display | ![]() |
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Full document | ![]() | 469.7 KB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Data in CIF | ![]() | 12.1 KB | Display | |
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Membrane protein | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |
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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: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 50.618133 KDa |
Recombinant expression | Organism: ![]() ![]() |
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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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |