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- PDB-9ukv: JM Complex - E. coli MurJ, Levivirus M lysis protein LysM (SglM) -

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Basic information

Entry
Database: PDB / ID: 9ukv
TitleJM Complex - E. coli MurJ, Levivirus M lysis protein LysM (SglM)
Components
  • Lipid II flippase MurJ
  • Lysis protein
KeywordsVIRAL PROTEIN / Phage / Lysis protein / Complex
Function / homology
Function and homology information


glycolipid translocation / lipid-linked peptidoglycan transport / viral release via suppression of host peptidoglycan biosynthetic process / lipid-linked peptidoglycan transporter activity / division septum / lipid translocation / cardiolipin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / plasma membrane
Similarity search - Function
Peptidoglycan biosynthesis protein MurJ / : / Lipid II flippase MurJ
Similarity search - Domain/homology
Lysis protein / Lipid II flippase MurJ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Enterobacteria phage M (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsKohga, H. / Lertpreedakorn, N. / Tsukazaki, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: JM Complex - E. coli MurJ, Levivirus M lysis protein LysM (SglM)
Authors: Kohga, H. / Lertpreedakorn, N. / Tsukazaki, T.
History
DepositionApr 18, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data 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
A: Lipid II flippase MurJ
B: Lysis protein


Theoretical massNumber of molelcules
Total (without water)63,6362
Polymers63,6362
Non-polymers00
Water00
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 Lipid II flippase MurJ / Peptidoglycan biosynthesis protein MurJ


Mass: 58100.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: murJ, mviN, yceN, b1069, JW1056 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AF16
#2: Protein/peptide Lysis protein


Mass: 5535.437 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage M (virus) / Gene: lys / Production host: Escherichia coli (E. coli) / References: UniProt: K7QK87
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: JM Complex - E. coli MurJ, Levivirus M lysis protein LysM (SglM)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 371016 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 156.12 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00254287
ELECTRON MICROSCOPYf_angle_d0.68595834
ELECTRON MICROSCOPYf_chiral_restr0.0384707
ELECTRON MICROSCOPYf_plane_restr0.0042707
ELECTRON MICROSCOPYf_dihedral_angle_d3.767583

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