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- PDB-9vuq: Structure of glycerol-3-phosphate acyltransferase PlsB from Themo... -

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Basic information

Entry
Database: PDB / ID: 9vuq
TitleStructure of glycerol-3-phosphate acyltransferase PlsB from Themomonas haemolytica in complex with Palmitoyl-CoA and DOPA
ComponentsGlycerol-3-phosphate acyltransferase
KeywordsLIPID TRANSPORT / Phospholipid synthesis / enzyme / Single-particle cryo-electron microscopy
Function / homology
Function and homology information


glycerol-3-phosphate 1-O-acyltransferase / glycerol-3-phosphate O-acyltransferase activity / CDP-diacylglycerol biosynthetic process / fatty acid metabolic process / plasma membrane
Similarity search - Function
Glycerol-3-phosphate acyltransferase PlsB N-terminal domain / Glycerol-3-phosphate O-acyltransferase/Dihydroxyacetone phosphate acyltransferase / Glycerol-3-phosphate acyltransferase, PlsB / GPAT/DHAPAT, acyltransferase domain / GPAT/DHAPAT, C-terminal domain / Glycerol-3-phosphate acyltransferase C-terminal region / Phospholipid/glycerol acyltransferase / Acyltransferase / Phosphate acyltransferases
Similarity search - Domain/homology
Chem-MX7 / Palmitoyl-CoA / Glycerol-3-phosphate acyltransferase
Similarity search - Component
Biological speciesThermomonas haemolytica (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsLi, Y.M. / Liu, X.Y. / Li, A.J. / Liu, Z.F.
Funding support China, 4items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37020101 China
Chinese Academy of SciencesYSBR-015 China
National Natural Science Foundation of China (NSFC)32430053 China
National Natural Science Foundation of China (NSFC)32000852 China
CitationJournal: Protein Sci. / Year: 2026
Title: The phospholipid biosynthesis enzyme PlsB contains three distinct domains for membrane association, lysophosphatidic acid synthesis, and dimerization
Authors: Li, Y. / Liu, X. / Li, A. / Liu, Z.
History
DepositionJul 13, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Glycerol-3-phosphate acyltransferase
C: Glycerol-3-phosphate acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,1476
Polymers199,7332
Non-polymers3,4144
Water36020
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Glycerol-3-phosphate acyltransferase / GPAT


Mass: 99866.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonas haemolytica (bacteria) / Gene: plsB, EDC34_102210 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A4R3N9S6, glycerol-3-phosphate 1-O-acyltransferase
#2: Chemical ChemComp-MX7 / (2R)-3-(phosphonooxy)propane-1,2-diyl (9Z,9'Z)bis-octadec-9-enoate / dioleoyl-phosphatidic acid


Mass: 700.966 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H73O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PKZ / Palmitoyl-CoA


Mass: 1005.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H66N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: P1sB with Palmitoyl CoA and 1,2-dioleoy1-sn-glycero-3-phosphate
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Themmomonas haemolytica
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1500 mMsodium chlorideNaCl1
22 mMDithiothreitolDTT1
35 mMEthylenediaminetetraaceticEDTA1
40.1 %Glyco-diogeninGDN1
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 291.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1300 nm / Cs: 2.7 mm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2PHENIX1.19.2_4158model refinement
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91865 / Symmetry type: POINT
RefinementHighest resolution: 2.79 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312104
ELECTRON MICROSCOPYf_angle_d0.5216410
ELECTRON MICROSCOPYf_dihedral_angle_d11.3274550
ELECTRON MICROSCOPYf_chiral_restr0.041816
ELECTRON MICROSCOPYf_plane_restr0.0042098

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