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- EMDB-24107: Cryo-EM structure of TACAN in the apo form (TMEM120A) -

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Basic information

Entry
Database: EMDB / ID: EMD-24107
TitleCryo-EM structure of TACAN in the apo form (TMEM120A)
Map data
Sample
  • Complex: Homo-dimeric assembly of wild type TACAN(TMEM120A)
    • Protein or peptide: Ion channel TACAN
Function / homology
Function and homology information


protein heterooligomerization / nuclear inner membrane / fat cell differentiation / detection of mechanical stimulus involved in sensory perception of pain / monoatomic ion transmembrane transport / protein homooligomerization / monoatomic ion channel activity / membrane / plasma membrane
Similarity search - Function
Ion channel TACAN/TMEM120B / TMPIT-like protein
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsNiu Y / Tao X / MacKinnon R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM43949 United States
CitationJournal: Elife / Year: 2021
Title: Analysis of the mechanosensor channel functionality of TACAN.
Authors: Yiming Niu / Xiao Tao / George Vaisey / Paul Dominic B Olinares / Hanan Alwaseem / Brian T Chait / Roderick MacKinnon /
Abstract: Mechanosensitive ion channels mediate transmembrane ion currents activated by mechanical forces. A mechanosensitive ion channel called TACAN was recently reported. We began to study TACAN with the ...Mechanosensitive ion channels mediate transmembrane ion currents activated by mechanical forces. A mechanosensitive ion channel called TACAN was recently reported. We began to study TACAN with the intent to understand how it senses mechanical forces and functions as an ion channel. Using cellular patch-recording methods, we failed to identify mechanosensitive ion channel activity. Using membrane reconstitution methods, we found that TACAN, at high protein concentrations, produces heterogeneous conduction levels that are not mechanosensitive and are most consistent with disruptions of the lipid bilayer. We determined the structure of TACAN using single-particle cryo-electron microscopy and observed that it is a symmetrical dimeric transmembrane protein. Each protomer contains an intracellular-facing cleft with a coenzyme A cofactor, confirmed by mass spectrometry. The TACAN protomer is related in three-dimensional structure to a fatty acid elongase, ELOVL7. Whilst its physiological function remains unclear, we anticipate that TACAN is not a mechanosensitive ion channel.
History
DepositionMay 25, 2021-
Header (metadata) releaseSep 15, 2021-
Map releaseSep 15, 2021-
UpdateSep 15, 2021-
Current statusSep 15, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.617
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.617
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7n0k
  • Surface level: 0.617
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24107.png

Downloads & links

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Map

FileDownload / File: emd_24107.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.617 / Movie #1: 0.617
Minimum - Maximum-2.801723 - 4.297385
Average (Standard dev.)0.0024489537 (±0.072657585)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 263.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z263.680263.680263.680
α/β/γ90.00090.00090.000
start NX/NY/NZ7371100
NX/NY/NZ11585169
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-2.8024.2970.002

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Supplemental data

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Sample components

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Entire : Homo-dimeric assembly of wild type TACAN(TMEM120A)

EntireName: Homo-dimeric assembly of wild type TACAN(TMEM120A)
Components
  • Complex: Homo-dimeric assembly of wild type TACAN(TMEM120A)
    • Protein or peptide: Ion channel TACAN

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Supramolecule #1: Homo-dimeric assembly of wild type TACAN(TMEM120A)

SupramoleculeName: Homo-dimeric assembly of wild type TACAN(TMEM120A) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Ion channel TACAN

MacromoleculeName: Ion channel TACAN / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 40.797297 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQSPPPDPLG DCLRNWEDLQ QDFQGIQETH RLYRLKLEEL TKLQANCTNS ITRQKKRLQE LALVLKKCRP SLPSESMEAA QELENQMKE RQGLFFDMEA YLPKKNGLYL SLVLGNVNVT LLSKQAKFAY KDEYEKFKLY LTIILIVISF TCRFLLNSRV T DAAFNFLL ...String:
MQSPPPDPLG DCLRNWEDLQ QDFQGIQETH RLYRLKLEEL TKLQANCTNS ITRQKKRLQE LALVLKKCRP SLPSESMEAA QELENQMKE RQGLFFDMEA YLPKKNGLYL SLVLGNVNVT LLSKQAKFAY KDEYEKFKLY LTIILIVISF TCRFLLNSRV T DAAFNFLL VWYYCTLTIR ESILINNGSR IKGWWVFHHY VSTFLSGVML TWPDGLMYQK FRNQFLSFSM YQSFVQFLQY YY QSGCLYR LRALGERHTM DLTVEGFQSW MWRGLTFLLP FLFFGHFWQL FNALTLFNLA RDPECKEWQV LMCGFPFLLL FLG NFFTTL RVVHQKFHSQ QHGNKKD

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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

Concentration6 mg/mL
BufferpH: 7.4
Details: 20 mM HEPES pH 7.4, 250 mM NaCl, and 0.06% Digitonin (w/v)
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Average exposure time: 10.0 sec. / Average electron dose: 75.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.0.6)
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Software: (Name: RELION (ver. 3.0), RELION (ver. 3.1), cryoSPARC (ver. 2.9.0))
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.9.0) / Number images used: 110090

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