+Open data
-Basic information
Entry | Database: PDB / ID: 8k0b | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of TMEM63C | ||||||
Components | Calcium permeable stress-gated cation channel 1 | ||||||
Keywords | MEMBRANE PROTEIN / Mechanosensitive ion channel | ||||||
Function / homology | Function and homology information osmolarity-sensing monoatomic cation channel activity / glomerular filtration / calcium-activated cation channel activity / monoatomic cation transport / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.56 Å | ||||||
Authors | Qin, Y. / Yu, D. / Dong, J. / Dang, S. | ||||||
Funding support | Hong Kong, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2023 Title: Cryo-EM structure of TMEM63C suggests it functions as a monomer. Authors: Yuqi Qin / Daqi Yu / Dan Wu / Jiangqing Dong / William Thomas Li / Chang Ye / Kai Chit Cheung / Yingyi Zhang / Yun Xu / YongQiang Wang / Yun Stone Shi / Shangyu Dang / Abstract: The TMEM63 family proteins (A, B, and C), calcium-permeable channels in animals that are preferentially activated by hypo-osmolality, have been implicated in various physiological functions. ...The TMEM63 family proteins (A, B, and C), calcium-permeable channels in animals that are preferentially activated by hypo-osmolality, have been implicated in various physiological functions. Deficiency of these channels would cause many diseases including hearing loss. However, their structures and physiological roles are not yet well understood. In this study, we determine the cryo-electron microscopy (cryo-EM) structure of the mouse TMEM63C at 3.56 Å, and revealed structural differences compared to TMEM63A, TMEM63B, and the plant orthologues OSCAs. Further structural guided mutagenesis and calcium imaging demonstrated the important roles of the coupling of TM0 and TM6 in channel activity. Additionally, we confirm that TMEM63C exists primarily as a monomer under physiological conditions, in contrast, TMEM63B is a mix of monomer and dimer in cells, suggesting that oligomerization is a regulatory mechanism for TMEM63 proteins. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8k0b.cif.gz | 137.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8k0b.ent.gz | 105 KB | Display | PDB format |
PDBx/mmJSON format | 8k0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k0b_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8k0b_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8k0b_validation.xml.gz | 31.9 KB | Display | |
Data in CIF | 8k0b_validation.cif.gz | 44.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/8k0b ftp://data.pdbj.org/pub/pdb/validation_reports/k0/8k0b | HTTPS FTP |
-Related structure data
Related structure data | 36759MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 93111.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tmem63c, CSC1 / Production host: Homo sapiens (human) / References: UniProt: Q8CBX0 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: TMEM63C / Type: CELL / Entity ID: all / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7 |
Specimen | Conc.: 1 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 R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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 / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 4.5 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 11058 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Particle selection | Num. of particles selected: 8754694 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 258464 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|