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- EMDB-54173: Cryo-EM structure of Shigella flexneri LptDE dimer: closed-state ... -

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Basic information

Entry
Database: EMDB / ID: EMD-54173
TitleCryo-EM structure of Shigella flexneri LptDE dimer: closed-state unbound and open-state bound by Oekolampad phage RBP
Map data
Sample
  • Complex: LptDE-RBP complex
    • Complex: LptDE
      • Protein or peptide: LPS-assembly protein LptD
      • Protein or peptide: LPS-assembly lipoprotein LptE
    • Complex: RBP
      • Protein or peptide: Tail fiber protein
Keywordslipopolysaccharide transport / receptor-binding protein / outer membrane protein complex / beta-barrel / 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
Protein of unknown function DUF6453 / Family of unknown function (DUF6453) / 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
Tail fiber protein / LPS-assembly lipoprotein LptE / LPS-assembly protein LptD
Similarity search - Component
Biological speciesShigella flexneri (bacteria) / Escherichia phage Oekolampad (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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_54173.png

Downloads & links

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Map

FileDownload / File: emd_54173.map.gz / Format: CCP4 / Size: 729 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 576 pix.
= 426.24 Å		0.74 Å/pix.
x 576 pix.
= 426.24 Å		0.74 Å/pix.
x 576 pix.
= 426.24 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: 0.09
Minimum - Maximum-0.24664672 - 0.4837809
Average (Standard dev.)0.0003376322 (±0.008688047)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 426.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54173_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_54173_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_54173_half_map_2.map
Projections & Slices
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Sample components

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Entire : LptDE-RBP complex

EntireName: LptDE-RBP complex
Components
  • Complex: LptDE-RBP complex
    • Complex: LptDE
      • Protein or peptide: LPS-assembly protein LptD
      • Protein or peptide: LPS-assembly lipoprotein LptE
    • Complex: RBP
      • Protein or peptide: Tail fiber protein

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Supramolecule #1: LptDE-RBP complex

SupramoleculeName: LptDE-RBP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: RBP

SupramoleculeName: RBP / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Escherichia phage Oekolampad (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: 2 / 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Shigella flexneri (bacteria)
Molecular weightTheoretical: 22.206471 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 TMLGNENLYF Q

UniProtKB: LPS-assembly lipoprotein LptE

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Macromolecule #3: Tail fiber protein

MacromoleculeName: Tail fiber protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Oekolampad (virus)
Molecular weightTheoretical: 35.347891 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGAGILIDYN DGRPRMEITA GLRAPSYCTS FNQRAQSNKT LTINTPLTAG SQVVVALTRP VEVIEVFDQT LVIPDPFYVT SVTRNGNSG ITLRGDDAYG AYSGLPQWAG VIMEVLPVGS RNAGLLVANS TDFTAISNVA KLMTCRYAKR VRVNGSMALP V SGVPFARW ...String:
MGAGILIDYN DGRPRMEITA GLRAPSYCTS FNQRAQSNKT LTINTPLTAG SQVVVALTRP VEVIEVFDQT LVIPDPFYVT SVTRNGNSG ITLRGDDAYG AYSGLPQWAG VIMEVLPVGS RNAGLLVANS TDFTAISNVA KLMTCRYAKR VRVNGSMALP V SGVPFARW DDGNVSVGFD GGSIIVRNAS YGGIDDVAAS VDMDLVIFNN TPPTPGTGIT MTNNQNQVTF STVNKPFVYD RT INIGTSD QNIGNSLIQL SYTGALIQNN GGYNHVRMNG IRMAGNNVRV AKNRVIGNYS RQQFQMPGKN IAVPTPLLVI PNM YHHHHH H

UniProtKB: Tail fiber protein

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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: 10744 / Average electron dose: 35.6 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 / Cs: 2.7 mm / 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: 1902801
CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 55494
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
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9rpw:
Cryo-EM structure of Shigella flexneri LptDE dimer: closed-state unbound and open-state bound by Oekolampad phage RBP

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