[English] 日本語
Yorodumi
- EMDB-21488: Human diacylglycerol O-acyltransferase 1 complex with oleoyl-CoA ... -

+
Open data


ID or keywords:

Loading...

-
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 1
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

-
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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21488.png

Downloads & links

-
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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
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

-
Supplemental data

-
Sample components

-
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 1

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 43.0 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

-
Image processing

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more