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- EMDB-65369: Structure of glycerol-3-phosphate acyltransferase PlsB from Themo... -

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Basic information

Entry
Database: EMDB / ID: EMD-65369
TitleStructure of glycerol-3-phosphate acyltransferase PlsB from Themomonas haemolytica in complex with Palmitoyl-CoA and DOPA
Map data
Sample
  • Complex: P1sB with Palmitoyl CoA and 1,2-dioleoy1-sn-glycero-3-phosphate
    • Protein or peptide: Glycerol-3-phosphate acyltransferase
  • Ligand: (2R)-3-(phosphonooxy)propane-1,2-diyl (9Z,9'Z)bis-octadec-9-enoate
  • Ligand: Palmitoyl-CoA
  • Ligand: water
KeywordsPhospholipid synthesis / enzyme / Single-particle cryo-electron microscopy / LIPID TRANSPORT
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
Glycerol-3-phosphate acyltransferase
Similarity search - Component
Biological speciesThemmomonas haemolytica (bacteria) / Thermomonas haemolytica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsLi YM / Liu XY / Li AJ / Liu ZF
Funding support China, 4 items
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: Yumei Li / Xiuying Liu / Anjie Li / Zhenfeng Liu /
Abstract: Biosynthesis of phospholipids is fundamental for membrane biogenesis in all living organisms. As a member of the glycerol-3-phosphate (G3P) acyltransferase family, PlsB is a crucial enzyme catalyzing ...Biosynthesis of phospholipids is fundamental for membrane biogenesis in all living organisms. As a member of the glycerol-3-phosphate (G3P) acyltransferase family, PlsB is a crucial enzyme catalyzing the first step of phospholipid synthesis by converting G3P and fatty acyl-coenzyme A (CoA)/acyl carrier protein (ACP) into lysophosphatidic acid and free CoA (CoASH)/ACP. In bacterial cells, PlsB participates in the formation of antibiotic-tolerant persister cells related to multidrug tolerance, and is hence considered as a potential target for anti-persister therapy. By using the single-particle cryo-electron microscopy method, we have solved the structure of full-length PlsB from Thermomonas haemolytica (ThPlsB) at 2.79 Å resolution. The ThPlsB protein forms a homodimer with C2 symmetry and each monomer contains three distinct domains, namely the amino-terminal domain (NTD), the middle catalytic domain (MCD), and the carboxy-terminal domain. In the MCD, a fatty acyl-CoA binds in a membrane-facing surface groove enclosed by a lipid molecule 1,2-dioleoyl-sn-glycero-3-phosphate (DOPA) on one side. The interactions between ThPlsB and the membrane involve four surface-exposed amphipathic regions located in the NTD and MCD, respectively. Our structural and biochemical analysis results suggest a membrane surface association-catalysis coupling model for the PlsB-mediated biosynthesis of lysophosphatidic acid occurring at the membrane-cytosol interface.
History
DepositionJul 13, 2025-
SupersessionJul 1, 2026ID: EMD-38558
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65369.png

Downloads & links

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Map

FileDownload / File: emd_65369.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0362
Minimum - Maximum-0.12162754 - 0.2349384
Average (Standard dev.)0.00012973692 (±0.003644256)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65369_msk_1.map
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Half map: #2

Fileemd_65369_half_map_1.map
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Half map: #1

Fileemd_65369_half_map_2.map
Projections & Slices
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Sample components

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Entire : P1sB with Palmitoyl CoA and 1,2-dioleoy1-sn-glycero-3-phosphate

EntireName: P1sB with Palmitoyl CoA and 1,2-dioleoy1-sn-glycero-3-phosphate
Components
  • Complex: P1sB with Palmitoyl CoA and 1,2-dioleoy1-sn-glycero-3-phosphate
    • Protein or peptide: Glycerol-3-phosphate acyltransferase
  • Ligand: (2R)-3-(phosphonooxy)propane-1,2-diyl (9Z,9'Z)bis-octadec-9-enoate
  • Ligand: Palmitoyl-CoA
  • Ligand: water

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Supramolecule #1: P1sB with Palmitoyl CoA and 1,2-dioleoy1-sn-glycero-3-phosphate

SupramoleculeName: P1sB with Palmitoyl CoA and 1,2-dioleoy1-sn-glycero-3-phosphate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Themmomonas haemolytica (bacteria)

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Macromolecule #1: Glycerol-3-phosphate acyltransferase

MacromoleculeName: Glycerol-3-phosphate acyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: glycerol-3-phosphate 1-O-acyltransferase
Source (natural)Organism: Thermomonas haemolytica (bacteria)
Molecular weightTheoretical: 99.866352 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAMPDRHSP DQPGLFDPPA AADDAATGPA GPAPLPLPGF LAADAATPPG PPSPPPAGKA RNPLWARLLG RLLAPWLRLE IEVDPAIAA DPRPICYVLE DYGLSNALIL QRACREAALP PPLQPIAGDP LGRRRAYVAL SRRHVNALGL LPGAEHKTHS G SLARLLQA ...String:
MAAMPDRHSP DQPGLFDPPA AADDAATGPA GPAPLPLPGF LAADAATPPG PPSPPPAGKA RNPLWARLLG RLLAPWLRLE IEVDPAIAA DPRPICYVLE DYGLSNALIL QRACREAALP PPLQPIAGDP LGRRRAYVAL SRRHVNALGL LPGAEHKTHS G SLARLLQA HQQQPELDVH LVPVSIFVGQ APKRSSGWFS VLFSENWTLV GRFRRLLAIL LNGRDTLVKF AAPVPVREIV AE GLEPERT VRKLSRILRT HFRRVREVVI GPDLSTRRML ADQVLSSPLV KEAIADQARR DGSKPEAAWE KANAYFWEIA ADY SNTVVR SASFALTFVW NRIYRGVLVH HLDQFKQEAP GHEVVYVPSH RSHMDYLLVS YLLYTHGVVP PHIFAGINLN LPVV GTLLR KGGAFFARRS FKGNALYSAV FREYMAQLVA GGYSIEYFIE GGRSRTGRLL QPKGGSLAMT VRAYLRQPTR PVLFQ PVYI GYEKLMEGRS YLDELSGKPK EKESIWQLLA GIPKVLRSNY GQVVVNFGER IQLSQVLAEL APEWDGQPIG DDEKPA WFA RTVDALAQRI QTNVNRAADV NPINLLALAL LSTPKHAMGE ADLRAQIALS KTLLAEVPYS DWVTVTPHTP EQIIAHG EE IGLITRTAHP LGDVLGVEGD NAVLLSYFRN NVLHLFTASS WIAVCFQNNR RMGRRQLQQI GRTLYPFLQA ELFLPWDE E TFAARIDRTI EVFVREGLLE QVSDEDGGIL QRNAGQSDEV FRLRALGHTL QQAFERYYIA IAILVKNGSG TLQAGELES LCQLTAQRLS LLYAPAAPEF FDKTLFRGFI QKLRELKLVW PDDTGRLAFD ERLKAWAKDA RVVLGRELRH TIEKISPAGS GRSSGEQPA LPPDPAATNG AS

UniProtKB: Glycerol-3-phosphate acyltransferase

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Macromolecule #2: (2R)-3-(phosphonooxy)propane-1,2-diyl (9Z,9'Z)bis-octadec-9-enoate

MacromoleculeName: (2R)-3-(phosphonooxy)propane-1,2-diyl (9Z,9'Z)bis-octadec-9-enoate
type: ligand / ID: 2 / Number of copies: 2 / Formula: MX7
Molecular weightTheoretical: 700.966 Da
Chemical component information

ChemComp-MX7:
(2R)-3-(phosphonooxy)propane-1,2-diyl (9Z,9'Z)bis-octadec-9-enoate

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Macromolecule #3: Palmitoyl-CoA

MacromoleculeName: Palmitoyl-CoA / type: ligand / ID: 3 / Number of copies: 2 / Formula: PKZ
Molecular weightTheoretical: 1.005943 KDa
Chemical component information

ChemComp-PKZ:
Palmitoyl-CoA

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 20 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration6 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
500.0 mMNaClsodium chloride
2.0 mMDTTDithiothreitol
5.0 mMEDTAEthylenediaminetetraacetic
0.1 %GDNGlyco-diogenin
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 291.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 91865
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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