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- EMDB-37852: cryo-EM structure of human TMEM63A -

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Basic information

Entry
Database: EMDB / ID: EMD-37852
Titlecryo-EM structure of human TMEM63A
Map datasharpen map
Sample
  • Complex: human TMEM63A
    • Protein or peptide: CSC1-like protein 1
Keywordsmechanically activated (MA) ion channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


surfactant secretion / osmolarity-sensing monoatomic cation channel activity / mechanosensitive monoatomic ion channel activity / calcium-activated cation channel activity / tertiary granule membrane / centriolar satellite / specific granule membrane / early endosome membrane / nucleic acid binding / lysosomal membrane ...surfactant secretion / osmolarity-sensing monoatomic cation channel activity / mechanosensitive monoatomic ion channel activity / calcium-activated cation channel activity / tertiary granule membrane / centriolar satellite / specific granule membrane / early endosome membrane / nucleic acid binding / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular exosome / 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 / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsYang D
Funding support China, 1 items
OrganizationGrant numberCountry
Other private China
CitationJournal: Proteins / Year: 2024
Title: A monomeric structure of human TMEM63A protein.
Authors: Xuening Wu / Tiantian Shang / Xinyi Lü / Deyi Luo / Dongxue Yang /
Abstract: OSCA/TMEM63 is a newly identified family of mechanically activated (MA) ion channels in plants and animals, respectively, which convert physical forces into electrical signals or trigger ...OSCA/TMEM63 is a newly identified family of mechanically activated (MA) ion channels in plants and animals, respectively, which convert physical forces into electrical signals or trigger intracellular cascades and are essential for eukaryotic physiology. OSCAs and related TMEM16s and transmembrane channel-like (TMC) proteins form homodimers with two pores. However, the molecular architecture of the mammalian TMEM63 proteins remains unclear. Here we elucidate the structure of human TMEM63A in the presence of calcium by single particle cryo-EM, revealing a distinct monomeric architecture containing eleven transmembrane helices. It has structural similarity to the single subunit of the Arabidopsis thaliana OSCA proteins. We locate the ion permeation pathway within the monomeric configuration and observe a nonprotein density resembling lipid. These results lay a foundation for understanding the structural organization of OSCA/TMEM63A family proteins.
History
DepositionOct 20, 2023-
Header (metadata) releaseJan 24, 2024-
Map releaseJan 24, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37852.png

Downloads & links

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Map

FileDownload / File: emd_37852.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpen map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.062 Å		1.1 Å/pix.
x 256 pix.
= 281.062 Å		1.1 Å/pix.
x 256 pix.
= 281.062 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.41
Minimum - Maximum-1.3805346 - 2.1642938
Average (Standard dev.)0.0027935093 (±0.05586403)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.0624 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpen map

Fileemd_37852_additional_1.map
Annotationunsharpen map
Projections & Slices
AxesZYX

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Histogram

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Half map: half map A

Fileemd_37852_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_37852_half_map_2.map
Annotationhalf map B
Projections & Slices
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Sample components

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Entire : human TMEM63A

EntireName: human TMEM63A
Components
  • Complex: human TMEM63A
    • Protein or peptide: CSC1-like protein 1

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Supramolecule #1: human TMEM63A

SupramoleculeName: human TMEM63A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: CSC1-like protein 1

MacromoleculeName: CSC1-like protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.331828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FLELWQSKAV SIREQLGLGD RPNDSYCYNS AKNSTVLQGV TFGGIPTVLL IDVSCFLFLI LVFSIIRRRF WDYGRIALVS EADSESRFQ RLSSTSSSGQ QDFENELGCC PWLTAIFRLH DDQILEWCGE DAIHYLSFQR HIIFLLVVVS FLSLCVILPV N LSGDLLDK ...String:
FLELWQSKAV SIREQLGLGD RPNDSYCYNS AKNSTVLQGV TFGGIPTVLL IDVSCFLFLI LVFSIIRRRF WDYGRIALVS EADSESRFQ RLSSTSSSGQ QDFENELGCC PWLTAIFRLH DDQILEWCGE DAIHYLSFQR HIIFLLVVVS FLSLCVILPV N LSGDLLDK DPYSFGRTTI ANLQTDNDLL WLHTIFAVIY LFLTVGFMRH HTQSIKYKEE NLVRRTLFIT GLPRDARKET VE SHFRDAY PTCEVVDVQL CYNVAKLIYL CKEKKKTEKS LTYYTNLQVK TGQRTLINPK PCGQFCCCEV LGCEWEDAIS YYT RMKDRL LERITEEERH VQDQPLGMAF VTFQEKSMAT YILKDFNACK CQSLQCKGEP QPSSHSRELY TSKWTVTFAA DPED ICWKN LSIQGLRWWL QWLGINFTLF LGLFFLTTPS IILSTMDKFN VTKPIHALNN PIISQFFPTL LLWSFSALLP SIVYY STLL ESHWTKSGEN QIMMTKVYIF LIFMVLILPS LGLTSLDFFF RWLFDKTSSE ASIRLECVFL PDQGAFFVNY VIASAF IGN GMELLRLPGL ILYTFRMIMA KTAADRRNVK QNQAFQYEFG AMYAWMLCVF TVIVAYSITC PIIAPFGLIY ILLKHMV DR HNLYFVYLPA KLEKGIHFAA VNQALAAPIL CLFWLYFFSF LRLGMKAPAT LFTFLVLLLT ILVCLAHTCF GC

UniProtKB: CSC1-like protein 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.56 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 163395
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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