+Open data
-Basic information
Entry | Database: PDB / ID: 6nph | ||||||
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Title | Structure of NKCC1 TM domain | ||||||
Components | Solute carrier family 12 (sodium/potassium/chloride transporter), member 2 | ||||||
Keywords | MEMBRANE PROTEIN | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Feng, L. / Liao, M.F. / Orlando, B. / Zhang, J.R. | ||||||
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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6nph.cif.gz | 168.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nph.ent.gz | 141.3 KB | Display | PDB format |
PDBx/mmJSON format | 6nph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nph_validation.pdf.gz | 986.8 KB | Display | wwPDB validaton report |
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Full document | 6nph_full_validation.pdf.gz | 1008.8 KB | Display | |
Data in XML | 6nph_validation.xml.gz | 39.4 KB | Display | |
Data in CIF | 6nph_validation.cif.gz | 56.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/6nph ftp://data.pdbj.org/pub/pdb/validation_reports/np/6nph | HTTPS FTP |
-Related structure data
Related structure data | 0470MC 0471C 0472C 0473C 0474C 0475C 6npjC 6npkC 6nplC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 50618.133 Da / Num. of mol.: 2 / Fragment: AA_permease domain, residues 206-677 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: slc12a2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0G2KGS0, UniProt: A0A0G2KTI4*PLUS #2: Chemical | ChemComp-POV / ( #3: Chemical | #4: Chemical | ChemComp-CL / |
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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: co-transporter transmembrane domain / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Danio rerio (zebrafish) | ||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 7.9 mg/ml / 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 R2/1 | ||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 96 % / Chamber temperature: 293 K |
-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 / Cs: 2.7 mm |
Image recording | Electron dose: 53 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
Image scans | Movie frames/image: 40 |
-Processing
EM software | Name: SerialEM / Category: image acquisition |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C2 (2 fold cyclic) |
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63659 / Symmetry type: POINT |
Atomic model building | Protocol: AB INITIO MODEL |