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- EMDB-50893: Cryo-EM structure of LptDE-YedD complex from Escherichia Coli -

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Basic information

Entry
Database: EMDB / ID: EMD-50893
TitleCryo-EM structure of LptDE-YedD complex from Escherichia Coli
Map dataCryo-EM electron density map of LptDE-YedD
Sample
  • Complex: LPS-assembly complex LptDE with lipoprotein YedD
    • Protein or peptide: LPS-assembly protein LptD
    • Protein or peptide: LPS-assembly lipoprotein LptE
    • Protein or peptide: Uncharacterized lipoprotein YedD
KeywordsOuter membrane protein / lipopolysaccharide transport (Lpt) complex / Lipid binding complex / LptDE Translocon / Lipocalin YedD. / 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 / plasma membrane
Similarity search - Function
YedD-like protein / YedD-like superfamily / YedD-like protein / LptD, C-terminal / LPS-assembly protein LptD / : / LPS transport system D / LPS-assembly lipoprotein LptE / Lipopolysaccharide-assembly / Organic solvent tolerance-like, N-terminal ...YedD-like protein / YedD-like superfamily / YedD-like protein / 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 YedD / LPS-assembly protein LptD
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsNguyen VS / Remaut H / Collet JF / Gennaris A / Thouvenel L
Funding support Belgium, 4 items
OrganizationGrant numberCountry
Fonds de la Recherche Scientifique (FNRS)WELBIO-CR-2015A-03 Belgium
Fonds de la Recherche Scientifique (FNRS)WELBIO-CR-2019C-03 Belgium
Research Foundation - Flanders (FWO)G0H5916N Belgium
Research Foundation - Flanders (FWO)12ZM421N Belgium
CitationJournal: Cell Rep / Year: 2025
Title: Optimal functioning of the Lpt bridge depends on a ternary complex between the lipocalin YedD and the LptDE translocon.
Authors: Alexandra Gennaris / Van Son Nguyen / Laurie Thouvenel / Naemi Csoma / Didier Vertommen / Bogdan Iuliu Iorga / Han Remaut / Jean-François Collet /
Abstract: The outer membrane is an efficient permeability barrier that protects gram-negative bacteria against external assaults, including many antibiotics. The unique permeability features of the outer ...The outer membrane is an efficient permeability barrier that protects gram-negative bacteria against external assaults, including many antibiotics. The unique permeability features of the outer membrane are due to the presence of lipopolysaccharide (LPS) molecules in its outer leaflet. LPS transport relies on the essential lipopolysaccharide transport (Lpt) pathway, which forms a bridge from the inner to the outer membrane. The LptDE translocon inserts LPS into the outer leaflet. Here, we identify the lipocalin YedD as a component of the translocon. Cryoelectron microscopy of the YedD-LptDE complex reveals that YedD binds LptD at a critical interface between its β-barrel and periplasmic β-taco domain. The YedD-LptDE complex is functionally relevant: under conditions where the connectivity of the β-taco and Lpt bridge is compromised, the absence of YedD decreases cell viability and causes LPS accumulation in the inner membrane. Our findings establish YedD as an Lpt component required for optimal LPS transport.
History
DepositionJul 4, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50893.png

Downloads & links

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Map

FileDownload / File: emd_50893.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM electron density map of LptDE-YedD
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 360 pix.
= 273.6 Å		0.76 Å/pix.
x 360 pix.
= 273.6 Å		0.76 Å/pix.
x 360 pix.
= 273.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.306486 - 2.1580803
Average (Standard dev.)0.0014089833 (±0.048655923)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 273.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50893_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half A

Fileemd_50893_half_map_1.map
AnnotationHalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half B

Fileemd_50893_half_map_2.map
AnnotationHalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LPS-assembly complex LptDE with lipoprotein YedD

EntireName: LPS-assembly complex LptDE with lipoprotein YedD
Components
  • Complex: LPS-assembly complex LptDE with lipoprotein YedD
    • Protein or peptide: LPS-assembly protein LptD
    • Protein or peptide: LPS-assembly lipoprotein LptE
    • Protein or peptide: Uncharacterized lipoprotein YedD

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Supramolecule #1: LPS-assembly complex LptDE with lipoprotein YedD

SupramoleculeName: LPS-assembly complex LptDE with lipoprotein YedD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The LptDE-YedD complex was purified from over-expression of the three components in E. coli. Strep-tag was on the C-terminal of LptE while his-tag was on the C-terminal of YedD. Double pull ...Details: The LptDE-YedD complex was purified from over-expression of the three components in E. coli. Strep-tag was on the C-terminal of LptE while his-tag was on the C-terminal of YedD. Double pull was done using 1, streptactin and 2, Ni-NTA.
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 120 KDa

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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: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 87.078438 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DLASQCMLGV PSYDRPLVQG DTNDLPVTIN ADHAKGDYPD DAVFTGSVDI MQGNSRLQAD EVQLHQKEAP GQPEPVRTVD ALGNVHYDD NQVILKGPKG WANLNTKDTN VWEGDYQMVG RQGRGKADLM KQRGENRYTI LDNGSFTSCL PGSDTWSVVG S EIIHDREE ...String:
DLASQCMLGV PSYDRPLVQG DTNDLPVTIN ADHAKGDYPD DAVFTGSVDI MQGNSRLQAD EVQLHQKEAP GQPEPVRTVD ALGNVHYDD NQVILKGPKG WANLNTKDTN VWEGDYQMVG RQGRGKADLM KQRGENRYTI LDNGSFTSCL PGSDTWSVVG S EIIHDREE QVAEIWNARF KVGPVPIFYS PYLQLPVGDK RRSGFLIPNA KYTTTNYFEF YLPYYWNIAP NMDATITPHY MH RRGNIMW ENEFRYLSQA GAGLMELDYL PSDKVYEDEH PNDDSSRRWL FYWNHSGVMD QVWRFNVDYT KVSDPSYFND FDN KYGSST DGYATQKFSV GYAVQNFNAT VSTKQFQVFS EQNTSSYSAE PQLDVNYYQN DVGPFDTRIY GQAVHFVNTR DDMP EATRV HLEPTINLPL SNNWGSINTE AKLLATHYQQ TNLDWYNSRN TTKLDESVNR VMPQFKVDGK MVFERDMEML APGYT QTLE PRAQYLYVPY RDQSDIYNYD SSLLQSDYSG LFRDRTYGGL DRIASANQVT TGVTSRIYDD AAVERFNISV GQIYYF TES RTGDDNITWE NDDKTGSLVW AGDTYWRISE RWGLRGGIQY DTRLDNVATS NSSIEYRRDE DRLVQLNYRY ASPEYIQ AT LPKYYSTAEQ YKNGISQVGA VASWPIADRW SIVGAYYYDT NANKQADSML GVQYSSCCYA IRVGYERKLN GWDNDKQH A VYDNAIGFNI ELRGLSSNYG LGTQEMLRSN ILPYQNTL

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: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 16.726266 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GWHLRDTTQV PSTMKVMILD SGDPNGPLSR AVRNQLRLNG VELLDKETTR KDVPSLRLGK VSIAKDTASV FRNGQTAEYQ MIMTVNATV LIPGRDIYPI SAKVFRSFFD NPQMALAKDN EQDMIVKEMY DRAAEQLIRK LPSIRAADIA

UniProtKB: LPS-assembly lipoprotein LptE

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Macromolecule #3: Uncharacterized lipoprotein YedD

MacromoleculeName: Uncharacterized lipoprotein YedD / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 12.999715 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
NYNNVVKTPA PDWLAGYWQT KGPQRALVSP EAIGSLIVTK EGDTLDCRQW QRVIAVPGKL TLMSDDLTNV TVKRELYEVE RDGNTIEYD GMTMERVDRP TAECAAALDK APLPTPLP

UniProtKB: Uncharacterized lipoprotein YedD

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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

Concentration2 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
20.0 mMTristrisaminomethane
150.0 mMNaClSodium Chloride
400.0 mMImidazoleImidazol
0.03 %DDMn-Dodecyl-Beta-Maltoside
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: GATAN CRYOPLUNGE 3 / Details: Blot 3-4 seconds.

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 13332 / Average exposure time: 3.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 60000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.55 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: models taken from Alphafold
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Software - details: Non-uniform refinement / Number images used: 56171
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 78.86
Output model

PDB-9fz5:
Cryo-EM structure of LptDE-YedD complex from Escherichia Coli

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