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Yorodumi- PDB-8h8e: Structure of the dimeric Xenopus tropical acid-sensitive outwardl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8h8e | ||||||
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Title | Structure of the dimeric Xenopus tropical acid-sensitive outwardly rectifying channel ASOR trimer bound with tRNA (closed state) | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Chloride Channel tRNA Complex | ||||||
Function / homology | pH-gated chloride channel activity / TMEM206 protein / TMEM206 protein family / chloride transport / chloride channel complex / plasma membrane / RNA / RNA (> 10) / Proton-activated chloride channel Function and homology information | ||||||
Biological species | Xenopus tropicalis (tropical clawed frog) Spodoptera frugiperda (fall armyworm) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.81 Å | ||||||
Authors | Chi, P. / Wang, X. / Li, J. / Li, K. / Zhang, Y. / Geng, J. / Wu, J. / Deng, D. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Res / Year: 2024 Title: Molecular insights into the inhibition of proton-activated chloride channel by transfer RNA. Authors: Pengliang Chi / Xiang Wang / Jialu Li / Hui Yang / Kaiju Li / Yuqi Zhang / Shiyi Lin / Leiye Yu / Shiqi Liu / Lu Chen / Ruobing Ren / Jianping Wu / Zhuo Huang / Jia Geng / Dong Deng / | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h8e.cif.gz | 351.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h8e.ent.gz | 284.8 KB | Display | PDB format |
PDBx/mmJSON format | 8h8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8h8e_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8h8e_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8h8e_validation.xml.gz | 63.8 KB | Display | |
Data in CIF | 8h8e_validation.cif.gz | 93.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/8h8e ftp://data.pdbj.org/pub/pdb/validation_reports/h8/8h8e | HTTPS FTP |
-Related structure data
Related structure data | 34544MC 8h8dC 8h8fC 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 |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 41031.789 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog) Gene: pacc1, tmem206 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q0V9Z3 #2: RNA chain | | Mass: 24108.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spodoptera frugiperda (fall armyworm) |
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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: Complex of Xenopus tropical acid-sensitive outwardly rectifying channel ASOR trimer and tRNA in digitonin Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Xenopus tropicalis (tropical clawed frog) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf9 |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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 / Nominal defocus max: 1800 nm / Nominal defocus min: 1100 nm |
Image recording | Electron dose: 57 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182807 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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