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- EMDB-31443: Lysophospholipid acyltransferase LPCAT3 in a complex with Arachid... -

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Basic information

Entry
Database: EMDB / ID: EMD-31443
TitleLysophospholipid acyltransferase LPCAT3 in a complex with Arachidonoyl-CoA
Map data
Sample
  • Complex: Lysophospholipid acyltransferase 5
    • Protein or peptide: LPCAT3
  • Ligand: S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenethioate
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
KeywordsLysophospholipid Acyltransferase / LPCAT3 / membrane-bound O-acyltransferase / cryo-EM / TRANSFERASE
Function / homology
Function and homology information


Acyl chain remodelling of PC / Acyl chain remodelling of PS / Acyl chain remodelling of PE / lysophospholipid acyltransferase activity / 1-acylglycerophosphocholine O-acyltransferase activity / lipid modification / phosphatidylcholine biosynthetic process / acyltransferase activity / membrane
Similarity search - Function
Membrane bound O-acyl transferase, MBOAT / MBOAT, membrane-bound O-acyltransferase family
Similarity search - Domain/homology
Lysophosphatidylcholine acyltransferase 3
Similarity search - Component
Biological speciesGallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsZhang Q / Yao D
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-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing 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-7f40
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31443.png

Downloads & links

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Map

FileDownload / File: emd_31443.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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.33 / Movie #1: 0.4
Minimum - Maximum-1.8839079 - 2.6910598
Average (Standard dev.)0.0056135403 (±0.06831461)
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-1.8842.6910.006

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Supplemental data

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Sample components

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Entire : Lysophospholipid acyltransferase 5

EntireName: Lysophospholipid acyltransferase 5
Components
  • Complex: Lysophospholipid acyltransferase 5
    • Protein or peptide: LPCAT3
  • Ligand: S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenethioate
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: Lysophospholipid acyltransferase 5

SupramoleculeName: Lysophospholipid acyltransferase 5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Gallus gallus (chicken)

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Macromolecule #1: LPCAT3

MacromoleculeName: LPCAT3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 57.26507 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGAERDESGA GAAVLVPLLG FGSNRPAGPA EKMAVAGSGW SLARVAEALG SSEQALRLIV SILMGYPFAL FQRYFLFQKE TYLIHLYNV FTGLSIAYFN FGMQFFHSLL CVLIQFLILR LMGRTVTAVF TTFVFQMTYL MAGYYFTATE HYDIKWTMPH C VLTLKLIG ...String:
MGAERDESGA GAAVLVPLLG FGSNRPAGPA EKMAVAGSGW SLARVAEALG SSEQALRLIV SILMGYPFAL FQRYFLFQKE TYLIHLYNV FTGLSIAYFN FGMQFFHSLL CVLIQFLILR LMGRTVTAVF TTFVFQMTYL MAGYYFTATE HYDIKWTMPH C VLTLKLIG LAIDYYDGGK DPELLTPEQR RFAVRGVPTL LEVSGFSYFY GAFMVGPQFS MTDYQKLAKG EMTDVPGQRP NS FVPALKR LSLGLLFLVT YTLSSPYISE EYLISDDYME KPFWFRCGYI LVWGKIILYK YVTCWLVTEG VCILVGLGYN GND QNGKPV WDACANMKVW LYETTPLFTG TIASFNINTN AWVARYVFKR LKFLGNKLLS QALALFFLAI WHGLHSGYLV CFQM ELLIV IVERQVINLV RDSPTLSTLA SITALQPIFY VLQQTNHWMF MGYSLVPFCL FTWDKWMKVY KSIYFLGHVL FFTLL LVLP YIRKLLVPRK EKLKKAE

UniProtKB: Lysophosphatidylcholine acyltransferase 3

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Macromolecule #2: S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidany...

MacromoleculeName: S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino] ...Name: S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenethioate
type: ligand / ID: 2 / Number of copies: 2 / Formula: 3IX
Molecular weightTheoretical: 1.053986 KDa
Chemical component information

ChemComp-3IX:
S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenethioate

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Macromolecule #3: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: PCW
Molecular weightTheoretical: 787.121 Da
Chemical component information

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

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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 K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 292613
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION

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