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Yorodumi- EMDB-34544: Structure of the dimeric Xenopus tropical acid-sensitive outwardl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34544 | |||||||||
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Title | Structure of the dimeric Xenopus tropical acid-sensitive outwardly rectifying channel ASOR trimer bound with tRNA (closed state) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Chloride Channel tRNA Complex / MEMBRANE PROTEIN | |||||||||
Function / homology | pH-gated chloride channel activity / TMEM206 protein / TMEM206 protein family / chloride transport / chloride channel complex / plasma membrane / Proton-activated chloride channel Function and homology information | |||||||||
Biological species | Xenopus tropicalis (tropical clawed frog) / Spodoptera frugiperda (fall armyworm) | |||||||||
Method | 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, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34544.map.gz | 230.1 MB | EMDB map data format | |
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Header (meta data) | emd-34544-v30.xml emd-34544.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
Images | emd_34544.png | 78.7 KB | ||
Filedesc metadata | emd-34544.cif.gz | 5.8 KB | ||
Others | emd_34544_half_map_1.map.gz emd_34544_half_map_2.map.gz | 226.3 MB 226.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34544 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34544 | HTTPS FTP |
-Validation report
Summary document | emd_34544_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_34544_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_34544_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | emd_34544_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34544 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34544 | HTTPS FTP |
-Related structure data
Related structure data | 8h8eMC 8h8dC 8h8fC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34544.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size |
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Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34544_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of Xenopus tropical acid-sensitive outwardly rectifying c...
Entire | Name: Complex of Xenopus tropical acid-sensitive outwardly rectifying channel ASOR trimer and tRNA in digitonin |
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Components |
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-Supramolecule #1: Complex of Xenopus tropical acid-sensitive outwardly rectifying c...
Supramolecule | Name: Complex of Xenopus tropical acid-sensitive outwardly rectifying channel ASOR trimer and tRNA in digitonin type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Xenopus tropicalis (tropical clawed frog) |
-Macromolecule #1: Proton-activated chloride channel
Macromolecule | Name: Proton-activated chloride channel / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus tropicalis (tropical clawed frog) |
Molecular weight | Theoretical: 41.031789 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MEAIRKELSR SYQELNEEAE PVAIDPEEAE DEEKEQEEAA SAVAPDRDSD RSSPPVRFSR TCLKNFFSVL LILVYLLLMG VAVFLVYQT ITDFRDKLKH PVMSVSYKEV NMYDAPGIAL YPGKARLLSC EHHWYDHIPP LKDPGQPGEN TCVTQDISYI D PYTNKTMK ...String: MEAIRKELSR SYQELNEEAE PVAIDPEEAE DEEKEQEEAA SAVAPDRDSD RSSPPVRFSR TCLKNFFSVL LILVYLLLMG VAVFLVYQT ITDFRDKLKH PVMSVSYKEV NMYDAPGIAL YPGKARLLSC EHHWYDHIPP LKDPGQPGEN TCVTQDISYI D PYTNKTMK HALIVQGPRD VRRRELVFLQ FHLNETKQDF SAIDYLLFSS YEAFLKSHDQ VKFMQDCESS FSSWKFSGGF RT WVKMSLV KTKEEDGSQS VEFRQETSVV NFIDRRETPD KGDQLFFVVF EWKDPYIQEI QDIITANPWS MIALLCSVFL VLF KAADFA KLSVKWMIKV RRRHLKKRAR ELNHIS UniProtKB: Proton-activated chloride channel |
-Macromolecule #2: tRNA (75-MER)of Spodoptera frugiperda
Macromolecule | Name: tRNA (75-MER)of Spodoptera frugiperda / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Spodoptera frugiperda (fall armyworm) |
Molecular weight | Theoretical: 24.108287 KDa |
Sequence | String: UCUUCGGUAG UAUAGUGGUC AGUAUCCCCG CCUGUCACGC GGGAGACCGG GGUUCGAUUC CCCGCCGGAG AGCCA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.1 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 182807 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |