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- EMDB-0831: Structure of the human sterol O-acyltransferase 1 in complex with... -

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Basic information

Entry
Database: EMDB / ID: EMD-0831
TitleStructure of the human sterol O-acyltransferase 1 in complex with CI-976
Map datasharpened map from cisTEM
Sample
  • Complex: human sterol O-acyltransferase 1 dimer
    • Protein or peptide: Sterol O-acyltransferase 1
  • Ligand: 2,2-dimethyl-N-(2,4,6-trimethoxyphenyl)dodecanamide
  • Ligand: CHOLESTEROL
KeywordsSOAT / ACAT / MBOAT / MEMBRANE PROTEIN / TRANSFERASE
Function / homology
Function and homology information


sterol O-acyltransferase / sterol O-acyltransferase activity / cholesterol O-acyltransferase activity / cholesterol storage / very-low-density lipoprotein particle assembly / positive regulation of amyloid precursor protein biosynthetic process / low-density lipoprotein particle clearance / fatty-acyl-CoA binding / LDL clearance / cholesterol efflux ...sterol O-acyltransferase / sterol O-acyltransferase activity / cholesterol O-acyltransferase activity / cholesterol storage / very-low-density lipoprotein particle assembly / positive regulation of amyloid precursor protein biosynthetic process / low-density lipoprotein particle clearance / fatty-acyl-CoA binding / LDL clearance / cholesterol efflux / cholesterol binding / macrophage derived foam cell differentiation / cholesterol metabolic process / cholesterol homeostasis / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding / membrane
Similarity search - Function
Sterol O-acyltransferase, metazoa / Sterol O-acyltransferase, ACAT/DAG/ARE types / Membrane bound O-acyl transferase, MBOAT / MBOAT, membrane-bound O-acyltransferase family
Similarity search - Domain/homology
Sterol O-acyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsChen L / Guan C
Funding support China, 5 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0502004 China
National Natural Science Foundation of China31622021 China
National Science Foundation (China)91857000 China
National Science Foundation (China)31821091 China
National Natural Science Foundation of China31870833 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) releaseApr 29, 2020-
Map releaseApr 29, 2020-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6l47
  • Surface level: 4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0831.png

Downloads & links

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Map

FileDownload / File: emd_0831.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map from cisTEM
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 200 pix.
= 209. Å		1.05 Å/pix.
x 200 pix.
= 209. Å		1.05 Å/pix.
x 200 pix.
= 209. 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: 4.0 / Movie #1: 4
Minimum - Maximum-8.535679999999999 - 13.942589
Average (Standard dev.)0.015068779 (±0.7130733)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 208.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0451.0451.045
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z209.000209.000209.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-8.53613.9430.015

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Supplemental data

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Additional map: 3.7A postprocesed map from relion

Fileemd_0831_additional.map
Annotation3.7A postprocesed map from relion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3.7A postprocesed map from relion

Fileemd_0831_additional_1.map
Annotation3.7A postprocesed map from relion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human sterol O-acyltransferase 1 dimer

EntireName: human sterol O-acyltransferase 1 dimer
Components
  • Complex: human sterol O-acyltransferase 1 dimer
    • Protein or peptide: Sterol O-acyltransferase 1
  • Ligand: 2,2-dimethyl-N-(2,4,6-trimethoxyphenyl)dodecanamide
  • Ligand: CHOLESTEROL

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Supramolecule #1: human sterol O-acyltransferase 1 dimer

SupramoleculeName: human sterol O-acyltransferase 1 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sterol O-acyltransferase 1

MacromoleculeName: Sterol O-acyltransferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: sterol O-acyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.294777 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKEVGSHFDD FVTNLIEKSA SLDNGGCALT TFSVLEGEKN NHRAKDLRAP PEQGKIFIAR RSLLDELLEV DHIRTIYHMF IALLILFIL STLVVDYIDE GRLVLEFSLL SYAFGKFPTV VWTWWIMFLS TFSVPYFLFQ HWATGYSKSS HPLIRSLFHG F LFMIFQIG ...String:
MKEVGSHFDD FVTNLIEKSA SLDNGGCALT TFSVLEGEKN NHRAKDLRAP PEQGKIFIAR RSLLDELLEV DHIRTIYHMF IALLILFIL STLVVDYIDE GRLVLEFSLL SYAFGKFPTV VWTWWIMFLS TFSVPYFLFQ HWATGYSKSS HPLIRSLFHG F LFMIFQIG VLGFGPTYVV LAYTLPPASR FIIIFEQIRF VMKAHSFVRE NVPRVLNSAK EKSSTVPIPT VNQYLYFLFA PT LIYRDSY PRNPTVRWGY VAMKFAQVFG CFFYVYYIFE RLCAPLFRNI KQEPFSARVL VLCVFNSILP GVLILFLTFF AFL HCWLNA FAEMLRFGDR MFYKDWWNST SYSNYYRTWN VVVHDWLYYY AYKDFLWFFS KRFKSAAMLA VFAVSAVVHE YALA VCLSF FYPVLFVLFM FFGMAFNFIV NDSRKKPIWN VLMWTSLFLG NGVLLCFYSQ EWYARQHCPL KNPTFLDYVR PRSWT CRYV F

UniProtKB: Sterol O-acyltransferase 1

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Macromolecule #2: 2,2-dimethyl-N-(2,4,6-trimethoxyphenyl)dodecanamide

MacromoleculeName: 2,2-dimethyl-N-(2,4,6-trimethoxyphenyl)dodecanamide / type: ligand / ID: 2 / Number of copies: 2 / Formula: E5L
Molecular weightTheoretical: 393.56 Da
Chemical component information

ChemComp-E5L:
2,2-dimethyl-N-(2,4,6-trimethoxyphenyl)dodecanamide

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Details: cisTEM resolution limiting methods / Number images used: 222018
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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