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- EMDB-54170: Cryo-EM structure of Shigella flexneri LptDE in complex with RTP4... -

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Basic information

Entry
Database: EMDB / ID: EMD-54170
TitleCryo-EM structure of Shigella flexneri LptDE in complex with RTP45 superinfection exclusion protein from RTP bacteriophage and endogenous LptM
Map data
Sample
  • Complex: LptDEM-RTP45 complex
    • Complex: LptDE
      • Protein or peptide: LPS-assembly protein LptD
      • Protein or peptide: LPS-assembly lipoprotein LptE
    • Complex: LptM
      • Protein or peptide: LPS-assembly lipoprotein LptM
    • Complex: RTP45
      • Protein or peptide: Phage lipoprotein
  • Ligand: PALMITIC ACID
  • Ligand: (2S)-propane-1,2-diyl dihexadecanoate
Keywordslipopolysaccharide transport / outer membrane complex / beta-barrel / superinfection exclusion / bacteriophage / MEMBRANE PROTEIN
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
LPS-assembly lipoprotein LptM / Phage lipoprotein / LPS-assembly lipoprotein LptE / LPS-assembly protein LptD
Similarity search - Component
Biological speciesShigella flexneri (bacteria) / Escherichia coli (E. coli) / Escherichia phage Rtp (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsDunbar E / Basle A / van den Berg B
Funding support United Kingdom, 2 items
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, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54170.png

Downloads & links

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Map

FileDownload / File: emd_54170.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 384 pix.
= 284.16 Å		0.74 Å/pix.
x 384 pix.
= 284.16 Å		0.74 Å/pix.
x 384 pix.
= 284.16 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.23055029 - 0.4759936
Average (Standard dev.)0.00047449014 (±0.011545214)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 284.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54170_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54170_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54170_half_map_2.map
Projections & Slices
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Sample components

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Entire : LptDEM-RTP45 complex

EntireName: LptDEM-RTP45 complex
Components
  • Complex: LptDEM-RTP45 complex
    • Complex: LptDE
      • Protein or peptide: LPS-assembly protein LptD
      • Protein or peptide: LPS-assembly lipoprotein LptE
    • Complex: LptM
      • Protein or peptide: LPS-assembly lipoprotein LptM
    • Complex: RTP45
      • Protein or peptide: Phage lipoprotein
  • Ligand: PALMITIC ACID
  • Ligand: (2S)-propane-1,2-diyl dihexadecanoate

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Supramolecule #1: LptDEM-RTP45 complex

SupramoleculeName: LptDEM-RTP45 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Shigella flexneri (bacteria)
Molecular weightTheoretical: 20.3 KDa

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Supramolecule #2: LptDE

SupramoleculeName: LptDE / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Shigella flexneri (bacteria)

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Supramolecule #3: LptM

SupramoleculeName: LptM / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #4: RTP45

SupramoleculeName: RTP45 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Escherichia phage Rtp (virus)

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Macromolecule #1: LPS-assembly protein LptD

MacromoleculeName: LPS-assembly protein LptD / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella flexneri (bacteria)
Molecular weightTheoretical: 89.740602 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEKRIPTLLA TMIATALYSQ QGLAADLASQ CMLGVPSYDR PLVQGDTNDL PVTINADHAK GDYPDDAVFT GSVDIMQGNS RLQADEVQL HQKEAPGQPE PVRTVDALGN VHYDDNQVIL KGPKGWANLN TKDTNVWEGD YQMVGRQGRG KADLMKQRGE N RYTILDNG ...String:
MEKRIPTLLA TMIATALYSQ QGLAADLASQ CMLGVPSYDR PLVQGDTNDL PVTINADHAK GDYPDDAVFT GSVDIMQGNS RLQADEVQL HQKEAPGQPE PVRTVDALGN VHYDDNQVIL KGPKGWANLN TKDTNVWEGD YQMVGRQGRG KADLMKQRGE N RYTILDNG SFTSCLPGSD TWSVVGSEII HDREEQVAEI WNARFKVGPV PIFYSPYLQL PVGDKRRSGF LIPNAKYTTT NY FEFYLPY YWNIAPNMDA TITPHYMHRR GNIMWENEFR YLSQAGAGLM ELDYLPSDKV YEDEHPNDDS SRRWLFYWNH SGV MDQVWR FNVDYTKVSD PSYFNDFDNK YGSSTDGYAT QKFSVGYAVQ NFNATVSTKQ FQVFSEQNTS SYSAEPQLDV NYYQ NDVGP FDTRIYGQAV HFVNTRDDMP EATRVHLEPT INLPLSNNWG SINTEAKFLA THYQQTNLDW YNSRNTTKLD ESVNR VMPQ FKVDGKMVFE RDMEMLAPGY TQTLEPRAQY LYVPYRDQSD IYNYDSSLLQ SDYSGLFRDR TYGGLDRIAS ANQVTT GVT SRIYDDAAVE RFNISVGQIY YFTESRTGDD NITWENDDKT GSLVWAGDTY WRISERWGLR GGIQYDTRLD NVATSNS SI EYRRDEDRLV QLNYHYASPE YIQATLPKYY STAEQYKNGI SQVGAVASRP IADRWSIVGA YYYDTNANKQ ADSMLGVQ Y SSCCYAIRVG YERKLNGWDN DKQHAVYDNA IGFNIELRGL SSNYGLGTQE MLRSNILPYQ NTL

UniProtKB: LPS-assembly protein LptD

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Macromolecule #2: LPS-assembly lipoprotein LptE

MacromoleculeName: LPS-assembly lipoprotein LptE / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shigella flexneri (bacteria)
Molecular weightTheoretical: 22.2405 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRYLATLLLS LAVLITAGCG WHLRDTTQVP STMKVMILDS GDPNGPLSRA VRNQLRLNGV ELLDKETTRK DVPSLRLGKV SIAKDTASV FRNGQTAEYQ MIMTVNATVL IPGRDIYPIS AKVFRSFFDN PQMALAKDNE QDMIVKEMYD RAAEQLIRKL P SIRAADIR ...String:
MRYLATLLLS LAVLITAGCG WHLRDTTQVP STMKVMILDS GDPNGPLSRA VRNQLRLNGV ELLDKETTRK DVPSLRLGKV SIAKDTASV FRNGQTAEYQ MIMTVNATVL IPGRDIYPIS AKVFRSFFDN PQMALAKDNE QDMIVKEMYD RAAEQLIRKL P SIRAADIR SDEEQTSTTT DTPATPARVS TMLGNHHHHH H

UniProtKB: LPS-assembly lipoprotein LptE

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Macromolecule #3: Phage lipoprotein

MacromoleculeName: Phage lipoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Rtp (virus)
Molecular weightTheoretical: 8.754979 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTNLIKLSII AAAAIMMVGC SSGPRPDGWC ATQASGVCVA KWKNGVVVPA GEVDVRYDGI KGSSGSVRDY GSKEWNHHHH HH

UniProtKB: Phage lipoprotein

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Macromolecule #4: LPS-assembly lipoprotein LptM

MacromoleculeName: LPS-assembly lipoprotein LptM / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 5.103607 KDa
SequenceString:
CGLKGPLYFP PADKNAPPPT KPVETQTQST VPDKNDRATG DGPSQVNY

UniProtKB: LPS-assembly lipoprotein LptM

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Macromolecule #5: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #6: (2S)-propane-1,2-diyl dihexadecanoate

MacromoleculeName: (2S)-propane-1,2-diyl dihexadecanoate / type: ligand / ID: 6 / Number of copies: 1 / Formula: PXS
Molecular weightTheoretical: 552.912 Da
Chemical component information

ChemComp-PXS:
(2S)-propane-1,2-diyl dihexadecanoate

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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: 7.5
Component:
ConcentrationFormulaName
10.0 mMC8H18N2O4SHEPES
100.0 mMNaClsodium chloride
0.05 (w/v) %C24H46O11DDM

Details: 10mM HEPES, pH7.5, 100mM NaCl, 0.05% (w/v) DDM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 11586 / Average electron dose: 50.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2178355
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71548
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9rps:
Cryo-EM structure of Shigella flexneri LptDE in complex with RTP45 superinfection exclusion protein from RTP bacteriophage and endogenous LptM

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