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- EMDB-31442: Lysophospholipid acyltransferase LPCAT3 in complex with lysophosp... -

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Basic information

Entry
Database: EMDB / ID: EMD-31442
TitleLysophospholipid acyltransferase LPCAT3 in complex with lysophosphatidylcholine
Map data
SampleLysophospholipid acyltransferase 5:
LPCAT3 / ligand
Function / homology
Function and homology information


lysophospholipid acyltransferase activity / positive regulation of triglyceride transport / positive regulation of sterol regulatory element binding protein cleavage / 1-acylglycerophosphoserine O-acyltransferase activity / 1-acylglycerophosphoethanolamine O-acyltransferase activity / Acyl chain remodelling of PE / Acyl chain remodelling of PS / Acyl chain remodelling of PC / positive regulation of intestinal cholesterol absorption / 1-acylglycerophosphocholine O-acyltransferase activity ...lysophospholipid acyltransferase activity / positive regulation of triglyceride transport / positive regulation of sterol regulatory element binding protein cleavage / 1-acylglycerophosphoserine O-acyltransferase activity / 1-acylglycerophosphoethanolamine O-acyltransferase activity / Acyl chain remodelling of PE / Acyl chain remodelling of PS / Acyl chain remodelling of PC / positive regulation of intestinal cholesterol absorption / 1-acylglycerophosphocholine O-acyltransferase activity / chylomicron assembly / phosphatidylserine acyl-chain remodeling / endoplasmic reticulum membrane organization / lipid modification / phosphatidylethanolamine acyl-chain remodeling / regulation of cholesterol biosynthetic process / intestinal stem cell homeostasis / phosphatidylcholine acyl-chain remodeling / negative regulation of response to endoplasmic reticulum stress / very-low-density lipoprotein particle assembly / phosphatidylcholine biosynthetic process / acyltransferase activity / negative regulation of inflammatory response / endoplasmic reticulum membrane / membrane / integral component of membrane
Similarity search - Function
Membrane bound O-acyl transferase, MBOAT / MBOAT, membrane-bound O-acyltransferase family
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesGallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsZhang Q / Yao D / Rao B / Li S / Jian L / Chen Y / Hu K / Xia Y / Shen Y / Cao Y
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFC1004704 China
National Natural Science Foundation of China (NSFC)8212500015 China
CitationJournal: Nat Commun / Year: 2021
Title: The structural basis for the phospholipid remodeling by lysophosphatidylcholine acyltransferase 3.
Authors: Qing Zhang / Deqiang Yao / Bing Rao / Liyan Jian / Yang Chen / Kexin Hu / Ying Xia / Shaobai Li / Yafeng Shen / An Qin / Jie Zhao / Lu Zhou / Ming Lei / Xian-Cheng Jiang / Yu Cao /
Abstract: As the major component of cell membranes, phosphatidylcholine (PC) is synthesized de novo in the Kennedy pathway and then undergoes extensive deacylation-reacylation remodeling via Lands' cycle. The ...As the major component of cell membranes, phosphatidylcholine (PC) is synthesized de novo in the Kennedy pathway and then undergoes extensive deacylation-reacylation remodeling via Lands' cycle. The re-acylation is catalyzed by lysophosphatidylcholine acyltransferase (LPCAT) and among the four LPCAT members in human, the LPCAT3 preferentially introduces polyunsaturated acyl onto the sn-2 position of lysophosphatidylcholine, thereby modulating the membrane fluidity and membrane protein functions therein. Combining the x-ray crystallography and the cryo-electron microscopy, we determined the structures of LPCAT3 in apo-, acyl donor-bound, and acyl receptor-bound states. A reaction chamber was revealed in the LPCAT3 structure where the lysophosphatidylcholine and arachidonoyl-CoA were positioned in two tunnels connected near to the catalytic center. A side pocket was found expanding the tunnel for the arachidonoyl CoA and holding the main body of arachidonoyl. The structural and functional analysis provides the basis for the re-acylation of lysophosphatidylcholine and the substrate preference during the reactions.
History
DepositionJun 17, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateDec 1, 2021-
Current statusDec 1, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7f3x
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_31442.map.gz / Format: CCP4 / Size: 76.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 272 pix.
= 233.92 Å
0.86 Å/pix.
x 272 pix.
= 233.92 Å
0.86 Å/pix.
x 272 pix.
= 233.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.4
Minimum - Maximum-1.3980991 - 2.4117775
Average (Standard dev.)0.0046854317 (±0.060521945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions272272272
Spacing272272272
CellA=B=C: 233.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z272272272
origin x/y/z0.0000.0000.000
length x/y/z233.920233.920233.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS272272272
D min/max/mean-1.3982.4120.005

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Supplemental data

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Sample components

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Entire Lysophospholipid acyltransferase 5

EntireName: Lysophospholipid acyltransferase 5 / Number of Components: 3

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Component #1: protein, Lysophospholipid acyltransferase 5

ProteinName: Lysophospholipid acyltransferase 5 / Recombinant expression: No
SourceSpecies: Gallus gallus (chicken)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, LPCAT3

ProteinName: LPCAT3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 57.26507 kDa
SourceSpecies: Gallus gallus (chicken)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: ligand, [2-((1-OXODODECANOXY-(2-HYDROXY-3-PROPANYL))-PHOSPHONATE-...

LigandName: [2-((1-OXODODECANOXY-(2-HYDROXY-3-PROPANYL))-PHOSPHONATE-OXY)-ETHYL]-TRIMETHYLAMMONIUM
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.440532 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen Name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 50 e/Å2 / Illumination Mode: SPOT SCAN
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 223896
3D reconstructionResolution: 3.57 Å / Resolution Method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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