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- EMDB-24230: Cryo-EM structure of human TMEM120A -

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Basic information

Entry
Database: EMDB / ID: EMD-24230
TitleCryo-EM structure of human TMEM120A
Map data
Sample
  • Complex: Human TMEM120A with CoA
    • Protein or peptide: Ion channel TACAN
  • Ligand: COENZYME A
KeywordsTransmembrane protein / 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 ...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 / membrane / plasma membrane
Similarity search - Function
Ion channel TACAN/TMEM120B / TMEM120A/B
Similarity search - Domain/homology
Transmembrane protein 120A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsJing JX / Yan YH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079179 United States
CitationJournal: Elife / Year: 2021
Title: TMEM120A is a coenzyme A-binding membrane protein with structural similarities to ELOVL fatty acid elongase.
Authors: Jing Xue / Yan Han / Hamid Baniasadi / Weizhong Zeng / Jimin Pei / Nick V Grishin / Junmei Wang / Benjamin P Tu / Youxing Jiang /
Abstract: TMEM120A, also named as TACAN, is a novel membrane protein highly conserved in vertebrates and was recently proposed to be a mechanosensitive channel involved in sensing mechanical pain. Here we ...TMEM120A, also named as TACAN, is a novel membrane protein highly conserved in vertebrates and was recently proposed to be a mechanosensitive channel involved in sensing mechanical pain. Here we present the single-particle cryogenic electron microscopy (cryo-EM) structure of human TMEM120A, which forms a tightly packed dimer with extensive interactions mediated by the N-terminal coiled coil domain (CCD), the C-terminal transmembrane domain (TMD), and the re-entrant loop between the two domains. The TMD of each TMEM120A subunit contains six transmembrane helices (TMs) and has no clear structural feature of a channel protein. Instead, the six TMs form an α-barrel with a deep pocket where a coenzyme A (CoA) molecule is bound. Intriguingly, some structural features of TMEM120A resemble those of elongase for very long-chain fatty acids (ELOVL) despite the low sequence homology between them, pointing to the possibility that TMEM120A may function as an enzyme for fatty acid metabolism, rather than a mechanosensitive channel.
History
DepositionJun 10, 2021-
Header (metadata) releaseSep 1, 2021-
Map releaseSep 1, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7n7p
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24230.png

Downloads & links

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Map

FileDownload / File: emd_24230.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 288 pix.
= 243.072 Å		0.84 Å/pix.
x 288 pix.
= 243.072 Å		0.84 Å/pix.
x 288 pix.
= 243.072 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.844 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.10388241 - 0.17417048
Average (Standard dev.)0.00021772992 (±0.004613607)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 243.07199 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8440.8440.844
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z243.072243.072243.072
α/β/γ90.00090.00090.000
start NX/NY/NZ127131139
NX/NY/NZ1079278
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.1040.1740.000

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Supplemental data

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Sample components

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Entire : Human TMEM120A with CoA

EntireName: Human TMEM120A with CoA
Components
  • Complex: Human TMEM120A with CoA
    • Protein or peptide: Ion channel TACAN
  • Ligand: COENZYME A

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Supramolecule #1: Human TMEM120A with CoA

SupramoleculeName: Human TMEM120A with CoA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: 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: Homo sapiens (human)
Molecular weightTheoretical: 42.013457 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG GSASQPPPPG PLGDCLRDWE DLQQDFQNIQ ETHRLYRLKL EELTKLQNNC TSSITRQKKR LQELALALKK CKPSLPAEA EGAAQELENQ MKERQGLFFD MEAYLPKKNG LYLSLVLGNV NVTLLSKQAK FAYKDEYEKF KLYLTIILIL I SFTCRFLL ...String:
MDYKDDDDKG GSASQPPPPG PLGDCLRDWE DLQQDFQNIQ ETHRLYRLKL EELTKLQNNC TSSITRQKKR LQELALALKK CKPSLPAEA EGAAQELENQ MKERQGLFFD MEAYLPKKNG LYLSLVLGNV NVTLLSKQAK FAYKDEYEKF KLYLTIILIL I SFTCRFLL NSRVTDAAFN FLLVWYYCTL TIRESILINN GSRIKGWWVF HHYVSTFLSG VMLTWPDGLM YQKFRNQFLS FS MYQSFVQ FLQYYYQSGC LYRLRALGER HTMDLTVEGF QSWMWRGLTF LLPFLFFGHF WQLFNALTLF NLAQDPQCKE WQV LMCGFP FLLLFLGNFF TTLRVVHHKF HSQRHGSKKD

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

BufferpH: 7.4
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: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 701283
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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