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Yorodumi- EMDB-28594: Human triacylglycerol synthesizing enzyme DGAT1 in complex with D... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28594 | |||||||||
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Title | Human triacylglycerol synthesizing enzyme DGAT1 in complex with DGAT1IN1 inhibitor | |||||||||
Map data | ||||||||||
Sample |
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Keywords | triglyceride biosynthesis / lipid storage / lipid metabolism / membrane protein / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information retinol O-fatty-acyltransferase / 2-acylglycerol O-acyltransferase activity / retinol O-fatty-acyltransferase activity / monoacylglycerol biosynthetic process / Triglyceride biosynthesis / diacylglycerol metabolic process / triglyceride biosynthetic process / Acyl chain remodeling of DAG and TAG / long-chain fatty-acyl-CoA metabolic process / diacylglycerol O-acyltransferase ...retinol O-fatty-acyltransferase / 2-acylglycerol O-acyltransferase activity / retinol O-fatty-acyltransferase activity / monoacylglycerol biosynthetic process / Triglyceride biosynthesis / diacylglycerol metabolic process / triglyceride biosynthetic process / Acyl chain remodeling of DAG and TAG / long-chain fatty-acyl-CoA metabolic process / diacylglycerol O-acyltransferase / diacylglycerol O-acyltransferase activity / very-low-density lipoprotein particle assembly / lipid storage / triglyceride metabolic process / acyltransferase activity / fatty acid homeostasis / specific granule membrane / Neutrophil degranulation / endoplasmic reticulum membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Sui X / Kun W / Walther T / Farese R / Liao M | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Mechanism of action for small-molecule inhibitors of triacylglycerol synthesis. Authors: Xuewu Sui / Kun Wang / Kangkang Song / Chen Xu / Jiunn Song / Chia-Wei Lee / Maofu Liao / Robert V Farese / Tobias C Walther / Abstract: Inhibitors of triacylglycerol (TG) synthesis have been developed to treat metabolism-related diseases, but we know little about their mechanisms of action. Here, we report cryo-EM structures of the ...Inhibitors of triacylglycerol (TG) synthesis have been developed to treat metabolism-related diseases, but we know little about their mechanisms of action. Here, we report cryo-EM structures of the TG-synthesis enzyme acyl-CoA:diacylglycerol acyltransferase 1 (DGAT1), a membrane bound O-acyltransferase (MBOAT), in complex with two different inhibitors, T863 and DGAT1IN1. Each inhibitor binds DGAT1's fatty acyl-CoA substrate binding tunnel that opens to the cytoplasmic side of the ER. T863 blocks access to the tunnel entrance, whereas DGAT1IN1 extends further into the enzyme, with an amide group interacting with more deeply buried catalytic residues. A survey of DGAT1 inhibitors revealed that this amide group may serve as a common pharmacophore for inhibition of MBOATs. The inhibitors were minimally active against the related MBOAT acyl-CoA:cholesterol acyltransferase 1 (ACAT1), yet a single-residue mutation sensitized ACAT1 for inhibition. Collectively, our studies provide a structural foundation for developing DGAT1 and other MBOAT inhibitors. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28594.map.gz | 59.9 MB | EMDB map data format | |
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Header (meta data) | emd-28594-v30.xml emd-28594.xml | 15 KB 15 KB | Display Display | EMDB header |
Images | emd_28594.png | 90.8 KB | ||
Masks | emd_28594_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-28594.cif.gz | 5.7 KB | ||
Others | emd_28594_half_map_1.map.gz emd_28594_half_map_2.map.gz | 48.5 MB 48.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28594 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28594 | HTTPS FTP |
-Validation report
Summary document | emd_28594_validation.pdf.gz | 978.8 KB | Display | EMDB validaton report |
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Full document | emd_28594_full_validation.pdf.gz | 978.4 KB | Display | |
Data in XML | emd_28594_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | emd_28594_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28594 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28594 | HTTPS FTP |
-Related structure data
Related structure data | 8etmMC 8esmC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_28594.map.gz / Format: CCP4 / Size: 64 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: 0.83 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_28594_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28594_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_28594_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CryoEM density of human diacylglycerol O-acyltransferase 1 in com...
Entire | Name: CryoEM density of human diacylglycerol O-acyltransferase 1 in complex with DGAT1IN1 inhibitor |
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Components |
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-Supramolecule #1: CryoEM density of human diacylglycerol O-acyltransferase 1 in com...
Supramolecule | Name: CryoEM density of human diacylglycerol O-acyltransferase 1 in complex with DGAT1IN1 inhibitor type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: CryoEM density of human diacylglycerol O-acyltransferase 1 in complex with DGAT1IN1 inhibitor |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Diacylglycerol O-acyltransferase 1
Macromolecule | Name: Diacylglycerol O-acyltransferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: diacylglycerol O-acyltransferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 55.339133 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGDRGSSRRR RTGSRPSSHG GGGPAAAEEE VRDAAAGPDV GAAGDAPAPA PNKDGDAGVG SGHWELRCHR LQDSLFSSDS GFSNYRGIL NWCVVMLILS NARLFLENLI KYGILVDPIQ VVSLFLKDPY SWPAPCLVIA ANVFAVAAFQ VEKRLAVGAL T EQAGLLLH ...String: MGDRGSSRRR RTGSRPSSHG GGGPAAAEEE VRDAAAGPDV GAAGDAPAPA PNKDGDAGVG SGHWELRCHR LQDSLFSSDS GFSNYRGIL NWCVVMLILS NARLFLENLI KYGILVDPIQ VVSLFLKDPY SWPAPCLVIA ANVFAVAAFQ VEKRLAVGAL T EQAGLLLH VANLATILCF PAAVVLLVES ITPVGSLLAL MAHTILFLKL FSYRDVNSWC RRARAKAASA GKKASSAAAP HT VSYPDNL TYRDLYYFLF APTLCYELNF PRSPRIRKRF LLRRILEMLF FTQLQVGLIQ QWMVPTIQNS MKPFKDMDYS RII ERLLKL AVPNHLIWLI FFYWLFHSCL NAVAELMQFG DREFYRDWWN SESVTYFWQN WNIPVHKWCI RHFYKPMLRR GSSK WMART GVFLASAFFH EYLVSVPLRM FRLWAFTGMM AQIPLAWFVG RFFQGNYGNA AVWLSLIIGQ PIAVLMYVHD YYVLN YEAP AAEA UniProtKB: Diacylglycerol O-acyltransferase 1 |
-Macromolecule #2: [(1S,4r)-4-{4-[(4S)-2-({[4-(trifluoromethoxy)phenyl]methyl}carbam...
Macromolecule | Name: [(1S,4r)-4-{4-[(4S)-2-({[4-(trifluoromethoxy)phenyl]methyl}carbamoyl)imidazo[1,2-a]pyridin-6-yl]phenyl}cyclohexyl]acetic acid type: ligand / ID: 2 / Number of copies: 2 / Formula: WTT |
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Molecular weight | Theoretical: 551.556 Da |
Chemical component information | ChemComp-WTT: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV |
Details | Protein sample was monodisperse. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14446 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |