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- EMDB-36759: Cryo-EM structure of TMEM63C -

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Basic information

Entry
Database: EMDB / ID: EMD-36759
TitleCryo-EM structure of TMEM63C
Map data
Sample
  • Cell: TMEM63C
    • Protein or peptide: Calcium permeable stress-gated cation channel 1
KeywordsMechanosensitive ion channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


osmolarity-sensing monoatomic cation channel activity / glomerular filtration / calcium-activated cation channel activity / endoplasmic reticulum membrane / plasma membrane
Similarity search - Function
CSC1/OSCA1-like, 7TM region / CSC1/OSCA1-like, cytosolic domain / CSC1/OSCA1-like, N-terminal transmembrane domain / Calcium permeable stress-gated cation channel 1-like / Calcium-dependent channel, 7TM region, putative phosphate / Late exocytosis, associated with Golgi transport / Cytosolic domain of 10TM putative phosphate transporter
Similarity search - Domain/homology
Calcium permeable stress-gated cation channel 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsQin Y / Yu D / Dong J / Dang S
Funding support Hong Kong, 1 items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)GRF16103321 Hong Kong
CitationJournal: 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
DepositionJul 8, 2023-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36759.png

Downloads & links

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Map

FileDownload / File: emd_36759.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.0016315937 - 2.2895775
Average (Standard dev.)0.0008530188 (±0.01990157)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36759_msk_1.map
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Half map: #2

Fileemd_36759_half_map_1.map
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Half map: #1

Fileemd_36759_half_map_2.map
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Sample components

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Entire : TMEM63C

EntireName: TMEM63C
Components
  • Cell: TMEM63C
    • Protein or peptide: Calcium permeable stress-gated cation channel 1

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Supramolecule #1: TMEM63C

SupramoleculeName: TMEM63C / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Calcium permeable stress-gated cation channel 1

MacromoleculeName: Calcium permeable stress-gated cation channel 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 93.111828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSAFPDSMDQ KFHNMTVNEC FQSRSTVLQG QPFGGIPTVL VLNIILWVFV VLLYSFLRKA AWDYGRLALL IHNDSLTSLI YGEQSEKSS PSEVSLEAER RDRGFSSWFF NSLTMRDRDL INKCGDDARI YITFQYHLII FVLILCIPSL GIILPVNYIG T VLDWNSHF ...String:
MSAFPDSMDQ KFHNMTVNEC FQSRSTVLQG QPFGGIPTVL VLNIILWVFV VLLYSFLRKA AWDYGRLALL IHNDSLTSLI YGEQSEKSS PSEVSLEAER RDRGFSSWFF NSLTMRDRDL INKCGDDARI YITFQYHLII FVLILCIPSL GIILPVNYIG T VLDWNSHF GRTTIVNVST ESKFLWLHSL FAFLYFLINL AFMGHHCLGF VPKKSLHFTR TLMITYVPTE IQDPEIISKH FH EAYPGCV VTRVHFCYDV RNLIDLDDQR RHAMRGRLYY TAKAKKTGKV MIKTHPCSRL CFCKCWTCFK EVDAEQYYSE LEE QLTDEF NAELNRVQLK RLDLIFVTFQ DARTVRRIYD DYKYIHCGRH PKQSSVTTIV KNYHWRVAHA PHPKDIIWKH LSIR RFSWW TRFIAINTFL FFLFFFLTTP AIIINTIDIY NVTRPIEKLQ SPIVTQFFPS VLLWAFTVTM PLLVYLSAFL EAHWT RSSQ NLIIVHKCYI FLVFMVVILP SMGLTSLHVF LRWLFDIYYL EHATIRFQCV FLPDNGAFFI NYVITAALLG TGMELM RLG SLCTYCTRLF LSKSEPERVH IRKNQATDFQ FGREYAWMLN VFSVVMAYSI TCPIIVPFGL LYLCMKHITD RYNMYYS YA PTKLNAQIHM AAVYQAIFAP LLGLFWMLFF SILRVGSLHS ITLFSMSSLI ISVVIAFSGV FLGKLRIAQR YEQPEEET E TVFDVEPSST TSTPTSLLYV ATVLQEPELN LTPASSPARH TYGTINSQPE EGEEESGLRG FARELDSAQF QEGLEMEGQ SH

UniProtKB: Calcium permeable stress-gated cation channel 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 11058 / Average exposure time: 4.5 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 8754694
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 258464
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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