+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24230 | |||||||||
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Title | Cryo-EM structure of human TMEM120A | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Transmembrane protein / MEMBRANE PROTEIN | |||||||||
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 channel activity / protein homooligomerization / monoatomic ion transmembrane transport / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.24 Å | |||||||||
Authors | Jing JX / Yan YH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_24230.map.gz | 84.8 MB | EMDB map data format | |
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Header (meta data) | emd-24230-v30.xml emd-24230.xml | 9.2 KB 9.2 KB | Display Display | EMDB header |
Images | emd_24230.png | 128 KB | ||
Filedesc metadata | emd-24230.cif.gz | 5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24230 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24230 | HTTPS FTP |
-Validation report
Summary document | emd_24230_validation.pdf.gz | 570.7 KB | Display | EMDB validaton report |
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Full document | emd_24230_full_validation.pdf.gz | 570.3 KB | Display | |
Data in XML | emd_24230_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_24230_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24230 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24230 | HTTPS FTP |
-Related structure data
Related structure data | 7n7pMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_24230.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.844 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Human TMEM120A with CoA
Entire | Name: Human TMEM120A with CoA |
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Components |
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-Supramolecule #1: Human TMEM120A with CoA
Supramolecule | Name: Human TMEM120A with CoA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Ion channel TACAN
Macromolecule | Name: Ion channel TACAN / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 42.013457 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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: Ion channel TACAN |
-Macromolecule #2: COENZYME A
Macromolecule | Name: COENZYME A / type: ligand / ID: 2 / Number of copies: 2 / Formula: COA |
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Molecular weight | Theoretical: 767.534 Da |
Chemical component information | ChemComp-COA: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 701283 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |