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- PDB-9rps: Cryo-EM structure of Shigella flexneri LptDE in complex with RTP4... -

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Basic information

Entry
Database: PDB / ID: 9rps
TitleCryo-EM structure of Shigella flexneri LptDE in complex with RTP45 superinfection exclusion protein from RTP bacteriophage and endogenous LptM
Components
  • (LPS-assembly lipoprotein ...) x 2
  • LPS-assembly protein LptD
  • Phage lipoprotein
KeywordsMEMBRANE PROTEIN / lipopolysaccharide transport / outer membrane complex / beta-barrel / superinfection exclusion / bacteriophage
Function / homology
Function and homology information


transporter complex / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / cell outer membrane / lipopolysaccharide binding
Similarity search - Function
: / Phage lipoprotein family / 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 ...: / Phage lipoprotein family / 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
PALMITIC ACID / (2S)-propane-1,2-diyl dihexadecanoate / LPS-assembly lipoprotein LptM / Phage lipoprotein / LPS-assembly lipoprotein LptE / LPS-assembly protein LptD
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
Escherichia phage Rtp (virus)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsDunbar, E. / Basle, A. / van den Berg, B.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)U-016275 IAA-CiC United Kingdom
Other private
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Small siphophage binding to an open state of the LptDE outer membrane lipopolysaccharide translocon.
Authors: Emily Dunbar / Robert Clark / Arnaud Baslé / Shenaz Allyjaun / Hector Newman / Julia Hubbard / Syma Khalid / Bert van den Berg /
Abstract: Bacteriophages are bacterial viruses that provide alternatives to small-molecule drugs to combat infections by antibiotic-resistant bacteria. To infect a bacterial host, a phage needs to bind to the ...Bacteriophages are bacterial viruses that provide alternatives to small-molecule drugs to combat infections by antibiotic-resistant bacteria. To infect a bacterial host, a phage needs to bind to the bacterial surface via receptor binding proteins (RBPs), which are critical for determining host specificity. For functionally important receptors, the RBP-receptor interaction could be exploited via phage steering, where emerging bacterial resistance due to receptor modification could make bacteria less fit or virulent. Despite this, relatively little is known about RBP-receptor interactions. Here, we build on the recent discovery of coliphages that have the outer membrane (OM) lipopolysaccharide translocon LptDE as their terminal receptor and show via cryogenic electron microscopy that, surprisingly, the RBP of the small siphophage Oekolampad binds to a hitherto unobserved, open state of LptDE. The open lateral gate of LptD is occupied by a β-strand peptide originating from the degraded N-terminal jellyroll domain of LptD, suggesting the possibility of LptD inhibition via peptidomimetics. A structure of LptDE in complex with the superinfection exclusion (SE) protein Rtp45 of the Oekolampad-related phage Rtp shows a mechanism of SE where Rtp45-induced conformational changes in LptD resulting from steric clashes preclude RBP binding. Finally, analysis of spontaneous Oekolampad-resistant mutants identifies mutations in LptD that abolish the LptDE-RBP interaction in vitro. SDS-EDTA sensitivity assays of the mutants show no major OM defects, consistent with largely preserved LptDE function, and suggesting that phage steering via LptDE might be challenging.
History
DepositionJun 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LPS-assembly protein LptD
B: LPS-assembly lipoprotein LptE
D: Phage lipoprotein
C: LPS-assembly lipoprotein LptM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,6496
Polymers125,8404
Non-polymers8092
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 2 molecules AD

#1: Protein LPS-assembly protein LptD


Mass: 89740.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: lptD, imp, ostA, SF0051, S0053 / Production host: Escherichia coli (E. coli) / References: UniProt: Q83SQ0
#3: Protein Phage lipoprotein


Mass: 8754.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Rtp (virus) / Gene: rtp45 / Production host: Escherichia coli (E. coli) / References: UniProt: Q333D9

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LPS-assembly lipoprotein ... , 2 types, 2 molecules BC

#2: Protein LPS-assembly lipoprotein LptE


Mass: 22240.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: lptE, rlpB, SF0640, S0662 / Production host: Escherichia coli (E. coli) / References: UniProt: Q83LX4
#4: Protein/peptide LPS-assembly lipoprotein LptM / LptD oxidative maturation-associated lipoprotein


Mass: 5103.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADN6

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#6: Chemical ChemComp-PXS / (2S)-propane-1,2-diyl dihexadecanoate


Mass: 552.912 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H68O4

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Details

Has ligand of interestN
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

Component
IDNameTypeEntity IDParent-IDSource
1LptDEM-RTP45 complexCOMPLEX#1-#40RECOMBINANT
2LptDECOMPLEX#1-#21RECOMBINANT
3LptMCOMPLEX#41NATURAL
4RTP45COMPLEX#31RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.1418 MDaNO
210.1073 MDaNO
310.0051 MDaNO
410.0068 MDaNO
510.0203 MDaNO
63
74
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Shigella flexneri (bacteria)623
32Shigella flexneri (bacteria)623
43Escherichia coli (E. coli)562
54Escherichia phage Rtp (virus)2994041
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
32Escherichia coli (E. coli)562
43Escherichia coli (E. coli)562
54Escherichia coli (E. coli)562
Buffer solutionpH: 7.5 / Details: 10mM HEPES, pH7.5, 100mM NaCl, 0.05% (w/v) DDM
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPESC8H18N2O4S1
2100 mMsodium chlorideNaCl1
30.05 (w/v) %DDMC24H46O111
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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 magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 50.6 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11586

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPU3.6image acquisition
7PHENIXmodel fitting
13Cootmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 2178355
3D reconstructionResolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71548 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model

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