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- EMDB-28552: Human Membrane-bound O-acyltransferase 7 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-28552
TitleHuman Membrane-bound O-acyltransferase 7
Map data
Sample
  • Complex: Membrane-bound O-acyltransferase 7
    • Protein or peptide: Lysophospholipid acyltransferase 7
Keywordslipid metabolism membrane remodeling / MEMBRANE PROTEIN
Function / homology
Function and homology information


2-acylglycerol-3-phosphate O-acyltransferase activity / 1-acylglycerol-3-phosphate O-acyltransferase activity / phosphatidylinositol acyl-chain remodeling / lysophospholipid acyltransferase activity / regulation of triglyceride metabolic process / lipid modification / phosphatidylcholine acyl-chain remodeling / O-acyltransferase activity / Acyl chain remodelling of PI / mitochondria-associated endoplasmic reticulum membrane contact site ...2-acylglycerol-3-phosphate O-acyltransferase activity / 1-acylglycerol-3-phosphate O-acyltransferase activity / phosphatidylinositol acyl-chain remodeling / lysophospholipid acyltransferase activity / regulation of triglyceride metabolic process / lipid modification / phosphatidylcholine acyl-chain remodeling / O-acyltransferase activity / Acyl chain remodelling of PI / mitochondria-associated endoplasmic reticulum membrane contact site / layer formation in cerebral cortex / ventricular system development / phosphatidylinositol biosynthetic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
Similarity search - Function
Membrane bound O-acyl transferase, MBOAT / MBOAT, membrane-bound O-acyltransferase family
Similarity search - Domain/homology
Lysophospholipid acyltransferase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang K / Liao M / Farese RV / Walther TC
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)R01GM141050 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2023
Title: The structure of phosphatidylinositol remodeling MBOAT7 reveals its catalytic mechanism and enables inhibitor identification.
Authors: Kun Wang / Chia-Wei Lee / Xuewu Sui / Siyoung Kim / Shuhui Wang / Aidan B Higgs / Aaron J Baublis / Gregory A Voth / Maofu Liao / Tobias C Walther / Robert V Farese /
Abstract: Cells remodel glycerophospholipid acyl chains via the Lands cycle to adjust membrane properties. Membrane-bound O-acyltransferase (MBOAT) 7 acylates lyso-phosphatidylinositol (lyso-PI) with ...Cells remodel glycerophospholipid acyl chains via the Lands cycle to adjust membrane properties. Membrane-bound O-acyltransferase (MBOAT) 7 acylates lyso-phosphatidylinositol (lyso-PI) with arachidonyl-CoA. MBOAT7 mutations cause brain developmental disorders, and reduced expression is linked to fatty liver disease. In contrast, increased MBOAT7 expression is linked to hepatocellular and renal cancers. The mechanistic basis of MBOAT7 catalysis and substrate selectivity are unknown. Here, we report the structure and a model for the catalytic mechanism of human MBOAT7. Arachidonyl-CoA and lyso-PI access the catalytic center through a twisted tunnel from the cytosol and lumenal sides, respectively. N-terminal residues on the ER lumenal side determine phospholipid headgroup selectivity: swapping them between MBOATs 1, 5, and 7 converts enzyme specificity for different lyso-phospholipids. Finally, the MBOAT7 structure and virtual screening enabled identification of small-molecule inhibitors that may serve as lead compounds for pharmacologic development.
History
DepositionOct 11, 2022-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateSep 27, 2023-
Current statusSep 27, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28552.png

Downloads & links

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Map

FileDownload / File: emd_28552.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.825 Å
Density
Contour LevelBy AUTHOR: 5.5
Minimum - Maximum-52.630023999999999 - 91.764139999999998
Average (Standard dev.)0.000000000002622 (±0.7150397)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 198.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_28552_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_28552_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Membrane-bound O-acyltransferase 7

EntireName: Membrane-bound O-acyltransferase 7
Components
  • Complex: Membrane-bound O-acyltransferase 7
    • Protein or peptide: Lysophospholipid acyltransferase 7

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Supramolecule #1: Membrane-bound O-acyltransferase 7

SupramoleculeName: Membrane-bound O-acyltransferase 7 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Purified protein
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55 kDa/nm

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Macromolecule #1: Lysophospholipid acyltransferase 7

MacromoleculeName: Lysophospholipid acyltransferase 7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.196277 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSPEEWTYLV VLLISIPIGF LFKKAGPGLK RWGAAAVGLG LTLFTCGPHT LHSLVTILGT WALIQAQPCS CHALALAWTF SYLLFFRAL SLLGLPTPTP FTNAVQLLLT LKLVSLASEV QDLHLAQRKE MASGFSKGPT LGLLPDVPSL METLSYSYCY V GIMTGPFF ...String:
MSPEEWTYLV VLLISIPIGF LFKKAGPGLK RWGAAAVGLG LTLFTCGPHT LHSLVTILGT WALIQAQPCS CHALALAWTF SYLLFFRAL SLLGLPTPTP FTNAVQLLLT LKLVSLASEV QDLHLAQRKE MASGFSKGPT LGLLPDVPSL METLSYSYCY V GIMTGPFF RYRTYLDWLE QPFPGAVPSL RPLLRRAWPA PLFGLLFLLS SHLFPLEAVR EDAFYARPLP ARLFYMIPVF FA FRMRFYV AWIAAECGCI AAGFGAYPVA AKARAGGGPT LQCPPPSSPE KAASLEYDYE TIRNIDCYST DFCVRVRDGM RYW NMTVQW WLAQYIYKSA PARSYVLRSA WTMLLSAYWH GLHPGYYLSF LTIPLCLAAE GRLESALRGR LSPGGQKAWD WVHW FLKMR AYDYMCMGFV LLSLADTLRY WASIYFCIHF LALAALGLGL ALGGGSPSRR KAASQPTSLA PEKLREELEA CGIEN LYFQ

UniProtKB: Lysophospholipid acyltransferase 7

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

Concentration6 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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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: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: Initial model were generated using ab initio construction in cryoSPARC
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 206418

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