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- EMDB-80861: Structure of glycerol-3-phosphate acyltransferase PlsB from Esche... -

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Basic information

Entry
Database: EMDB / ID: EMD-80861
TitleStructure of glycerol-3-phosphate acyltransferase PlsB from Escherichia coli
Map data
Sample
  • Complex: Escherichia coli PlsB
    • Protein or peptide: Glycerol-3-phosphate acyltransferase
KeywordsPhospholipid synthesis / enzyme / Single-particle cryo-electron microscopy / MEMBRANE PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.22 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: Li Y / Liu X / Li A / Liu Z
History
DepositionMay 14, 2026-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80861.png

Downloads & links

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Map

FileDownload / File: emd_80861.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.037958127 - 0.06217343
Average (Standard dev.)0.00006293029 (±0.0011549661)
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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Half map: #1

Fileemd_80861_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_80861_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 : Escherichia coli PlsB

EntireName: Escherichia coli PlsB
Components
  • Complex: Escherichia coli PlsB
    • Protein or peptide: Glycerol-3-phosphate acyltransferase

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Supramolecule #1: Escherichia coli PlsB

SupramoleculeName: Escherichia coli PlsB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Glycerol-3-phosphate acyltransferase

MacromoleculeName: Glycerol-3-phosphate acyltransferase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: glycerol-3-phosphate 1-O-acyltransferase
SequenceString: MSGWPRIYYK LLNLPLSILV KSKSIPADPA PELGLDTSRP IMYVLPYNSK ADLLTLRAQC LAHDLPDPLE PLEIDGTLL PRYVFIHGGP RVFTYYTPKE ESIKLFHDYL DLHRSNPNLD VQMVPVSVMF GRAPGREKGE V NPPLRMLN GVQKFFAVLW LGRDSFVRFS ...String:
MSGWPRIYYK LLNLPLSILV KSKSIPADPA PELGLDTSRP IMYVLPYNSK ADLLTLRAQC LAHDLPDPLE PLEIDGTLL PRYVFIHGGP RVFTYYTPKE ESIKLFHDYL DLHRSNPNLD VQMVPVSVMF GRAPGREKGE V NPPLRMLN GVQKFFAVLW LGRDSFVRFS PSVSLRRMAD EHGTDKTIAQ KLARVARMHF ARQRLAAVGP RLPARQDLFN KLLASRAIAK AVEDEARSKK ISHEKAQQNA IALMEEIAAN FSYEMIRLTD RILGFTWNRL YQ GINVHNA ERVRQLAHDG HELVYVPCHR SHMDYLLLSY VLYHQGLVPP HIAAGINLNF WPAGPIFRRL GAF FIRRTF KGNKLYSTVF REYLGELFSR GYSVEYFVEG GRSRTGRLLD PKTGTLSMTI QAMLRGGTRP ITLI PIYIG YEHVMEVGTY AKELRGATKE KESLPQMLRG LSKLRNLGQG YVNFGEPMPL MTYLNQHVPD WRESI DPIE AVRPAWLTPT VNNIAADLMV RINNAGAANA MNLCCTALLA SRQRSLTREQ LTEQLNCYLD LMRNVPYSTD STVPSASASE LIDHALQMNK FEVEKDTIGD IIILPREQAV LMTYYRNNIA HMLVLPSLMA AIVTQH RHI SRDVLMEHVN VLYPMLKAEL FLRWDRDELP DVIDALANEM QRQGLITLQD DELHINPAHS RTLQLLA AG ARETLQRYAI TFWLLSANPS INRGTLEKES RTVAQRLSVL HGINAPEFFD KAVFSSLVLT LRDEGYIS D SGDAEPAETM KVYQLLAELI TSDVRLTIES ATQGEG

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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: 8
VitrificationCryogen name: ETHANE

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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: 4.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 44196
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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