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- EMDB-0830: Structure of the human sterol O-acyltransferase 1 tetramer in rho... -

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Basic information

Entry
Database: EMDB / ID: EMD-0830
TitleStructure of the human sterol O-acyltransferase 1 tetramer in rhombic shape
Map data
Sample
  • Complex: human sterol O-acyltransferase 1 tetramer
    • Protein or peptide: Structure of the human sterol O-acyltransferase 1
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.6 Å
AuthorsChen L / Guan C
Funding support China, 5 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0502004 China
National Science Foundation (China)91857000 China
National Natural Science Foundation of China31622021 China
National Natural Science Foundation of China31870833 China
National Science Foundation (China)31821091 China
CitationJournal: Nat Commun / Year: 2020
Title: Structural insights into the inhibition mechanism of human sterol O-acyltransferase 1 by a competitive inhibitor.
Authors: Chengcheng Guan / Yange Niu / Si-Cong Chen / Yunlu Kang / Jing-Xiang Wu / Koji Nishi / Catherine C Y Chang / Ta-Yuan Chang / Tuoping Luo / Lei Chen /
Abstract: Sterol O-acyltransferase 1 (SOAT1) is an endoplasmic reticulum (ER) resident, multi-transmembrane enzyme that belongs to the membrane-bound O-acyltransferase (MBOAT) family. It catalyzes the ...Sterol O-acyltransferase 1 (SOAT1) is an endoplasmic reticulum (ER) resident, multi-transmembrane enzyme that belongs to the membrane-bound O-acyltransferase (MBOAT) family. It catalyzes the esterification of cholesterol to generate cholesteryl esters for cholesterol storage. SOAT1 is a target to treat several human diseases. However, its structure and mechanism remain elusive since its discovery. Here, we report the structure of human SOAT1 (hSOAT1) determined by cryo-EM. hSOAT1 is a tetramer consisted of a dimer of dimer. The structure of hSOAT1 dimer at 3.5 Å resolution reveals that a small molecule inhibitor CI-976 binds inside the catalytic chamber and blocks the accessibility of the active site residues H460, N421 and W420. Our results pave the way for future mechanistic study and rational drug design targeting hSOAT1 and other mammalian MBOAT family members.
History
DepositionOct 16, 2019-
Header (metadata) releaseOct 7, 2020-
Map releaseOct 7, 2020-
UpdateOct 7, 2020-
Current statusOct 7, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0830.png

Downloads & links

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Map

FileDownload / File: emd_0830.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 180 pix.
= 188.1 Å		1.05 Å/pix.
x 180 pix.
= 188.1 Å		1.05 Å/pix.
x 180 pix.
= 188.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.023
Minimum - Maximum-0.03674565 - 0.09946824
Average (Standard dev.)0.0008503583 (±0.007884176)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 188.09999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0451.0451.045
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z188.100188.100188.100
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0370.0990.001

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Supplemental data

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Sample components

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Entire : human sterol O-acyltransferase 1 tetramer

EntireName: human sterol O-acyltransferase 1 tetramer
Components
  • Complex: human sterol O-acyltransferase 1 tetramer
    • Protein or peptide: Structure of the human sterol O-acyltransferase 1

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Supramolecule #1: human sterol O-acyltransferase 1 tetramer

SupramoleculeName: human sterol O-acyltransferase 1 tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293T

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Macromolecule #1: Structure of the human sterol O-acyltransferase 1

MacromoleculeName: Structure of the human sterol O-acyltransferase 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MVGEEKMSLR NRLSKSRENP EEDEDQRNPA KESLETPSNG RIDIKQLIAK KIKLTAEAEE LKPFFMKEVG SHFDDFVTNL IEKSASLDN GGCALTTFSV LEGEKNNHRA KDLRAPPEQG KIFIARRSLL DELLEVDHIR TIYHMFIALL ILFILSTLVV D YIDEGRLV ...String:
MVGEEKMSLR NRLSKSRENP EEDEDQRNPA KESLETPSNG RIDIKQLIAK KIKLTAEAEE LKPFFMKEVG SHFDDFVTNL IEKSASLDN GGCALTTFSV LEGEKNNHRA KDLRAPPEQG KIFIARRSLL DELLEVDHIR TIYHMFIALL ILFILSTLVV D YIDEGRLV LEFSLLSYAF GKFPTVVWTW WIMFLSTFSV PYFLFQHWAT GYSKSSHPLI RSLFHGFLFM IFQIGVLGFG PT YVVLAYT LPPASRFIII FEQIRFVMKA HSFVRENVPR VLNSAKEKSS TVPIPTVNQY LYFLFAPTLI YRDSYPRNPT VRW GYVAMK FAQVFGCFFY VYYIFERLCA PLFRNIKQEP FSARVLVLCV FNSILPGVLI LFLTFFAFLH CWLNAFAEML RFGD RMFYK DWWNSTSYSN YYRTWNVVVH DWLYYYAYKD FLWFFSKRFK SAAMLAVFAV SAVVHEYALA VCLSFFYPVL FVLFM FFGM AFNFIVNDSR KKPIWNVLMW TSLFLGNGVL LCFYSQEWYA RQHCPLKNPT FLDYVRPRSW TCRYVF

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 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

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 13703
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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