[English] 日本語
Yorodumi- PDB-5tqq: Cryo-electron microscopy structure of a bovine CLC-K chloride cha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tqq | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-electron microscopy structure of a bovine CLC-K chloride channel, main (class 1) conformation | |||||||||
Components |
| |||||||||
Keywords | TRANSPORT PROTEIN / CLC / chloride channel / membrane / kidney | |||||||||
Function / homology | Function and homology information Stimuli-sensing channels / voltage-gated chloride channel activity / chloride transport / membrane Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) Mus musculus (house mouse) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.76 Å | |||||||||
Authors | Park, E. / MacKinnon, R. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Nature / Year: 2017 Title: Structure of a CLC chloride ion channel by cryo-electron microscopy. Authors: Eunyong Park / Ernest B Campbell / Roderick MacKinnon / Abstract: CLC proteins transport chloride (Cl) ions across cellular membranes to regulate muscle excitability, electrolyte movement across epithelia, and acidification of intracellular organelles. Some CLC ...CLC proteins transport chloride (Cl) ions across cellular membranes to regulate muscle excitability, electrolyte movement across epithelia, and acidification of intracellular organelles. Some CLC proteins are channels that conduct Cl ions passively, whereas others are secondary active transporters that exchange two Cl ions for one H. The structural basis underlying these distinctive transport mechanisms is puzzling because CLC channels and transporters are expected to share the same architecture on the basis of sequence homology. Here we determined the structure of a bovine CLC channel (CLC-K) using cryo-electron microscopy. A conserved loop in the Cl transport pathway shows a structure markedly different from that of CLC transporters. Consequently, the cytosolic constriction for Cl passage is widened in CLC-K such that the kinetic barrier previously postulated for Cl/H transporter function would be reduced. Thus, reduction of a kinetic barrier in CLC channels enables fast flow of Cl down its electrochemical gradient. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5tqq.cif.gz | 318.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5tqq.ent.gz | 261.4 KB | Display | PDB format |
PDBx/mmJSON format | 5tqq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tqq_validation.pdf.gz | 917.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5tqq_full_validation.pdf.gz | 930.1 KB | Display | |
Data in XML | 5tqq_validation.xml.gz | 48.9 KB | Display | |
Data in CIF | 5tqq_validation.cif.gz | 76.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/5tqq ftp://data.pdbj.org/pub/pdb/validation_reports/tq/5tqq | HTTPS FTP |
-Related structure data
Related structure data | 8435MC 8454C 5tr1C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 73521.484 Da / Num. of mol.: 2 / Mutation: N373Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: LOC101909378 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: E1B792 #2: Antibody | Mass: 11824.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma 25E7 / Production host: Mus musculus (house mouse) #3: Antibody | Mass: 12633.068 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): hybridoma 25E7 / Production host: Mus musculus (house mouse) |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: A bovine CLC-K channel complexed with a monoclonal antibody fragment (Fab) Type: COMPLEX Details: Fab fragment generated by proteolytic (papain) cleavage of murine IgG antibody. Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Bos taurus (cattle) | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Plasmid: pFastBac (BacMam) | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||||||||||||
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 295 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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 | Average exposure time: 0.3 sec. / Electron dose: 1.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: REFMAC / Version: 5.8.0088 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82167 Details: the indicated resolution was estimated on the primary map using the provided mask including Fab. Symmetry type: POINT |