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- PDB-9kn3: Cryo-EM structure of LptDEM complex from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 9kn3
TitleCryo-EM structure of LptDEM complex from Escherichia coli
Components
  • LPS-assembly lipoprotein LptE
  • LPS-assembly protein LptD
  • Uncharacterized lipoprotein YifL
KeywordsMEMBRANE PROTEIN / LPS / Transporter / Complex
Function / homology
Function and homology information


transporter complex / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / cell outer membrane / lipopolysaccharide binding / plasma membrane
Similarity search - Function
Prokaryotic lipoprotein-attachment site / LPS-assembly lipoprotein LptM, conserved region / LptD, C-terminal / LPS-assembly protein LptD / : / LPS transport system D / LPS-assembly lipoprotein LptE / Lipopolysaccharide-assembly / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
LPS-assembly lipoprotein LptE / Uncharacterized lipoprotein YifL / LPS-assembly protein LptD
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsTsukazaki, T. / Kohga, H. / Miyazaki, R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Cell Rep / Year: 2025
Title: Structural basis of lipopolysaccharide translocon assembly mediated by the small lipoprotein LptM
Authors: Miyazaki, R. / Kimoto, M. / Kohga, H. / Tsukazaki, T.
History
DepositionNov 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LPS-assembly protein LptD
B: LPS-assembly lipoprotein LptE
C: Uncharacterized lipoprotein YifL


Theoretical massNumber of molelcules
Total (without water)113,3563
Polymers113,3563
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 LPS-assembly protein LptD / Organic solvent tolerance protein


Mass: 87149.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lptD, imp, ostA, yabG, b0054, JW0053 / Production host: Escherichia coli (E. coli) / References: UniProt: P31554
#2: Protein LPS-assembly lipoprotein LptE / Rare lipoprotein B


Mass: 19479.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lptE, rlpB, b0641, JW0636 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADC1
#3: Protein Uncharacterized lipoprotein YifL


Mass: 6727.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: yifL, b4558, JW3781 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADN6
Has protein modificationY

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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: LptDEM complex in Nanodisc / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 4.648 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: -1600 nm / Nominal defocus min: -600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 428907 / Symmetry type: POINT
Atomic model buildingB value: 108.5 / Protocol: AB INITIO MODEL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 72.57 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00927572
ELECTRON MICROSCOPYf_angle_d0.691810294
ELECTRON MICROSCOPYf_chiral_restr0.04991079
ELECTRON MICROSCOPYf_plane_restr0.00561365
ELECTRON MICROSCOPYf_dihedral_angle_d4.87711031

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