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- EMDB-24108: Cryo-EM structure of TACAN in the H196A H197A mutant form (TMEM120A) -

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Basic information

Entry
Database: EMDB / ID: EMD-24108
TitleCryo-EM structure of TACAN in the H196A H197A mutant form (TMEM120A)
Map data
Sample
  • Complex: Homo-dimeric assembly of H196A H197A mutant TACAN(TMEM120A)
    • Protein or peptide: Ion channel TACAN
  • Ligand: COENZYME A
Keywordslipid metabolism / coenzyme A / MEMBRANE PROTEIN
Function / homology
Function and homology information


coenzyme A binding / protein heterooligomerization / nuclear inner membrane / fat cell differentiation / monoatomic ion channel activity / detection of mechanical stimulus involved in sensory perception of pain / antiviral innate immune response / protein homooligomerization / monoatomic ion transmembrane transport / endoplasmic reticulum / plasma membrane
Similarity search - Function
Ion channel TACAN/TMEM120B / TMEM120A/B
Similarity search - Domain/homology
Transmembrane protein 120A
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsNiu Y / Tao X
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-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0224
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0224
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7n0l
  • Surface level: 0.0224
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24108.png

Downloads & links

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Map

FileDownload / File: emd_24108.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 256 pix.
= 263.68 Å		1.03 Å/pix.
x 256 pix.
= 263.68 Å		1.03 Å/pix.
x 256 pix.
= 263.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0224 / Movie #1: 0.0224
Minimum - Maximum-0.06545487 - 0.14596337
Average (Standard dev.)0.000007002511 (±0.004492239)
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-0.0650.1460.000

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Supplemental data

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Sample components

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Entire : Homo-dimeric assembly of H196A H197A mutant TACAN(TMEM120A)

EntireName: Homo-dimeric assembly of H196A H197A mutant TACAN(TMEM120A)
Components
  • Complex: Homo-dimeric assembly of H196A H197A mutant TACAN(TMEM120A)
    • Protein or peptide: Ion channel TACAN
  • Ligand: COENZYME A

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Supramolecule #1: Homo-dimeric assembly of H196A H197A mutant TACAN(TMEM120A)

SupramoleculeName: Homo-dimeric assembly of H196A H197A mutant TACAN(TMEM120A)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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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: 40.66316 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 IKGWWVFAAY VSTFLSGVML TWPDGLMYQK FRNQFLSFSM YQSFVQFLQY YY QSGCLYR LRALGERHTM DLTVEGFQSW MWRGLTFLLP FLFFGHFWQL FNALTLFNLA RDPECKEWQV LMCGFPFLLL FLG NFFTTL RVVHQKFHSQ QHGNKKD

UniProtKB: Transmembrane protein 120A

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Macromolecule #2: COENZYME A

MacromoleculeName: COENZYME A / type: ligand / ID: 2 / Number of copies: 2 / Formula: COA
Molecular weightTheoretical: 767.534 Da
Chemical component information

ChemComp-COA:
COENZYME A

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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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 1.5 sec. / Average electron dose: 56.6 e/Å2
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.9.0) / Number images used: 155946
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Software: (Name: RELION (ver. 3.0), RELION (ver. 3.1), cryoSPARC (ver. 2.9.0))
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.1)

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