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- EMDB-21488: Human diacylglycerol O-acyltransferase 1 complex with oleoyl-CoA ... -

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Basic information

Entry
Database: EMDB / ID: EMD-21488
TitleHuman diacylglycerol O-acyltransferase 1 complex with oleoyl-CoA that shows a cleaved acyl-CoA signal
Map dataHuman diacylglycerol O-acyltransferase 1 complexed with oleoyl-CoA showing broken acyl-CoA density
Sample
  • Complex: human diacylglycerol O-acyltransferase 1 complexed with a cleaved acyl-CoA substrate
    • Protein or peptide: human diacylglycerol O-acyltransferase 1Diglyceride acyltransferase
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsSui X / Wang K / Gluchowski N / Liao M / Walther CT
Funding support United States, 4 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM097194 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM124348 United States
American Heart Association18POST34030308 United States
CitationJournal: Nature / Year: 2020
Title: Structure and catalytic mechanism of a human triacylglycerol-synthesis enzyme.
Authors: Xuewu Sui / Kun Wang / Nina L Gluchowski / Shane D Elliott / Maofu Liao / Tobias C Walther / Robert V Farese /
Abstract: Triacylglycerols store metabolic energy in organisms and have industrial uses as foods and fuels. Excessive accumulation of triacylglycerols in humans causes obesity and is associated with metabolic ...Triacylglycerols store metabolic energy in organisms and have industrial uses as foods and fuels. Excessive accumulation of triacylglycerols in humans causes obesity and is associated with metabolic diseases. Triacylglycerol synthesis is catalysed by acyl-CoA diacylglycerol acyltransferase (DGAT) enzymes, the structures and catalytic mechanisms of which remain unknown. Here we determined the structure of dimeric human DGAT1, a member of the membrane-bound O-acyltransferase (MBOAT) family, by cryo-electron microscopy at approximately 3.0 Å resolution. DGAT1 forms a homodimer through N-terminal segments and a hydrophobic interface, with putative active sites within the membrane region. A structure obtained with oleoyl-CoA substrate resolved at approximately 3.2 Å shows that the CoA moiety binds DGAT1 on the cytosolic side and the acyl group lies deep within a hydrophobic channel, positioning the acyl-CoA thioester bond near an invariant catalytic histidine residue. The reaction centre is located inside a large cavity, which opens laterally to the membrane bilayer, providing lipid access to the active site. A lipid-like density-possibly representing an acyl-acceptor molecule-is located within the reaction centre, orthogonal to acyl-CoA. Insights provided by the DGAT1 structures, together with mutagenesis and functional studies, provide the basis for a model of the catalysis of triacylglycerol synthesis by DGAT.
History
DepositionFeb 28, 2020-
Header (metadata) releaseApr 1, 2020-
Map releaseMay 20, 2020-
UpdateJun 3, 2020-
Current statusJun 3, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21488.png

Downloads & links

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Map

FileDownload / File: emd_21488.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman diacylglycerol O-acyltransferase 1 complexed with oleoyl-CoA showing broken acyl-CoA density
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.13685943 - 0.23318006
Average (Standard dev.)0.00016324782 (±0.008842201)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z212.480212.480212.480
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ350350350
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1370.2330.000

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Supplemental data

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Sample components

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Entire : human diacylglycerol O-acyltransferase 1 complexed with a cleaved...

EntireName: human diacylglycerol O-acyltransferase 1 complexed with a cleaved acyl-CoA substrate
Components
  • Complex: human diacylglycerol O-acyltransferase 1 complexed with a cleaved acyl-CoA substrate
    • Protein or peptide: human diacylglycerol O-acyltransferase 1Diglyceride acyltransferase

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Supramolecule #1: human diacylglycerol O-acyltransferase 1 complexed with a cleaved...

SupramoleculeName: human diacylglycerol O-acyltransferase 1 complexed with a cleaved acyl-CoA substrate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: From cryoEM density of human diacylglycerol O-acyltransferase 1 complexed with oleoyl-CoA substrate showing broken oleoyl-CoA density
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant plasmid: pFasBacMam

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Macromolecule #1: human diacylglycerol O-acyltransferase 1

MacromoleculeName: human diacylglycerol O-acyltransferase 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: diacylglycerol O-acyltransferase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGDRGSSRRR RTGSRPSSHG GGGPAAAEEE VRDAAAGPDV GAAGDAPAPA PNKDGDAGVG SGHWELRCHR LQDSLFSSD SGFSNYRGIL NWCVVMLILS NARLFLENLI KYGILVDPIQ VVSLFLKDPY SWPAPCLVIA A NVFAVAAF QVEKRLAVGA LTEQAGLLLH ...String:
MGDRGSSRRR RTGSRPSSHG GGGPAAAEEE VRDAAAGPDV GAAGDAPAPA PNKDGDAGVG SGHWELRCHR LQDSLFSSD SGFSNYRGIL NWCVVMLILS NARLFLENLI KYGILVDPIQ VVSLFLKDPY SWPAPCLVIA A NVFAVAAF QVEKRLAVGA LTEQAGLLLH VANLATILCF PAAVVLLVES ITPVGSLLAL MAHTILFLKL FS YRDVNSW CRRARAKAAS AGKKASSAAA PHTVSYPDNL TYRDLYYFLF APTLCYELNF PRSPRIRKRF LLR RILEML FFTQLQVGLI QQWMVPTIQN SMKPFKDMDY SRIIERLLKL AVPNHLIWLI FFYWLFHSCL NAVA ELMQF GDREFYRDWW NSESVTYFWQ NWNIPVHKWC IRHFYKPMLR RGSSKWMART GVFLASAFFH EYLVS VPLR MFRLWAFTGM MAQIPLAWFV GRFFQGNYGN AAVWLSLIIG QPIAVLMYVH DYYVLNYEAP AAEA

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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

Concentration5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: GATAN CRYOPLUNGE 3
DetailsProtein sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 43.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27750

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