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- PDB-8h8e: Structure of the dimeric Xenopus tropical acid-sensitive outwardl... -

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Basic information

Entry
Database: PDB / ID: 8h8e
TitleStructure of the dimeric Xenopus tropical acid-sensitive outwardly rectifying channel ASOR trimer bound with tRNA (closed state)
Components
  • Proton-activated chloride channel
  • tRNA (75-MER)of Spodoptera frugiperda
KeywordsMEMBRANE PROTEIN / Chloride Channel tRNA Complex
Function / homologypH-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 speciesXenopus tropicalis (tropical clawed frog)
Spodoptera frugiperda (fall armyworm)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsChi, P. / Wang, X. / Li, J. / Li, K. / Zhang, Y. / Geng, J. / Wu, J. / Deng, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971132 China
CitationJournal: 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
DepositionOct 22, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proton-activated chloride channel
B: Proton-activated chloride channel
C: Proton-activated chloride channel
D: Proton-activated chloride channel
E: Proton-activated chloride channel
F: Proton-activated chloride channel
G: tRNA (75-MER)of Spodoptera frugiperda


Theoretical massNumber of molelcules
Total (without water)270,2997
Polymers270,2997
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Proton-activated chloride channel / PAC / Transmembrane protein 206


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 tRNA (75-MER)of Spodoptera frugiperda


Mass: 24108.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spodoptera frugiperda (fall armyworm)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of Xenopus tropical acid-sensitive outwardly rectifying channel ASOR trimer and tRNA in digitonin
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Xenopus tropicalis (tropical clawed frog)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf9
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 57 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182807 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00316385
ELECTRON MICROSCOPYf_angle_d0.60622517
ELECTRON MICROSCOPYf_dihedral_angle_d12.232767
ELECTRON MICROSCOPYf_chiral_restr0.0412517
ELECTRON MICROSCOPYf_plane_restr0.0042553

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