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- PDB-9rlc: LolCDE complex with Lpp lipoprotein -

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Basic information

Entry
Database: PDB / ID: 9rlc
TitleLolCDE complex with Lpp lipoprotein
Components
  • (Lipoprotein-releasing system transmembrane protein ...) x 2
  • Lipoprotein-releasing system ATP-binding protein LolD
  • Major outer membrane lipoprotein Lpp
KeywordsPROTEIN TRANSPORT / Gram-negative / envelope biogenesis / outer membrane protein
Function / homology
Function and homology information


periplasmic space organization / lipid modification / lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / lipoprotein transport / peptidoglycan binding / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / transmembrane transporter activity ...periplasmic space organization / lipid modification / lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / lipoprotein transport / peptidoglycan binding / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / cell outer membrane / transmembrane transport / outer membrane-bounded periplasmic space / lipid binding / ATP hydrolysis activity / extracellular region / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
Lipoprotein leucine-zipper / Major outer membrane lipoprotein Lpp / Lipoprotein leucine-zipper / Lipoprotein releasing system, ATP-binding protein / Lipoprotein-releasing system transmembrane protein LolE, gammaproteobacteria type / Lipoprotein release ATP-binding protein lolD family profile. / Lipoprotein-releasing system transmembrane protein LolC/E / : / MacB-like periplasmic core domain / MacB-like periplasmic core domain ...Lipoprotein leucine-zipper / Major outer membrane lipoprotein Lpp / Lipoprotein leucine-zipper / Lipoprotein releasing system, ATP-binding protein / Lipoprotein-releasing system transmembrane protein LolE, gammaproteobacteria type / Lipoprotein release ATP-binding protein lolD family profile. / Lipoprotein-releasing system transmembrane protein LolC/E / : / MacB-like periplasmic core domain / MacB-like periplasmic core domain / ABC transporter, lipoprotein release, LolD / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease C-terminal / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PALMITIC ACID / (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate / Lipoprotein-releasing system transmembrane protein LolC / Major outer membrane lipoprotein Lpp / Lipoprotein-releasing system ATP-binding protein LolD / Lipoprotein-releasing system transmembrane protein LolE
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsSymmons, M.F. / Szewczyk, P. / Greene, N.P. / Hardwick, S.W. / Koronakis, V.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V000616/1 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Liganded LolCDE structures reveal a common substrate-LolE interaction guiding bacterial lipoprotein transport.
Authors: Paul Szewczyk / Nicholas P Greene / Martyn F Symmons / Steven W Hardwick / Vassilis Koronakis /
Abstract: Bacterial lipoproteins are key structural components of the outer membrane in Gram-negative bacteria and vital components of machineries required for its biosynthesis and maintenance. The Lol system, ...Bacterial lipoproteins are key structural components of the outer membrane in Gram-negative bacteria and vital components of machineries required for its biosynthesis and maintenance. The Lol system, essential for viability, directs transport of lipoproteins from the site of biosynthesis on the inner membrane to the outer membrane and has been the target of extensive efforts to develop novel antimicrobial drugs. In the first stage of this transport process, newly synthesized lipoproteins are released from the inner membrane by the ABC transporter LolCDE and passed to the periplasmic chaperone, LolA. Here, we show cryo-EM structures of LolCDE in complex with three different lipoprotein substrates, Lpp, Pal, and LolB, with the latter two bearing a disordered peptide linker between the acyl chains and the globular domain. Our work reveals that when the mature lipoprotein lacks an unstructured linker, the N-terminal portion of the protein is in an unfolded state for transport. The lipoproteins make a sequence-independent but structurally conserved interaction with a cleft on the surface of the periplasmic domain of LolE that promotes efficient transport. We propose a model of lipoprotein export where this interaction acts as pivot point for the peptide portion of the lipoprotein allowing the acyl chains to rotate 180° from their initial position in LolCDE to their binding site in LolA. Our results demonstrate how LolCDE can extrude lipoproteins of diverse sequence and structure and reveal an important detail of a transport process fundamental to bacterial physiology.
History
DepositionJun 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.1Feb 4, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Lipoprotein-releasing system transmembrane protein LolC
E: Lipoprotein-releasing system transmembrane protein LolE
D: Lipoprotein-releasing system ATP-binding protein LolD
F: Lipoprotein-releasing system ATP-binding protein LolD
L: Major outer membrane lipoprotein Lpp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,8117
Polymers148,9855
Non-polymers8252
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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Lipoprotein-releasing system transmembrane protein ... , 2 types, 2 molecules CE

#1: Protein Lipoprotein-releasing system transmembrane protein LolC


Mass: 43295.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lolC, ycfU, b1116, JW5161 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0ADC3
#2: Protein Lipoprotein-releasing system transmembrane protein LolE


Mass: 45385.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lolE, ycfW, b1118, JW1104 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P75958

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Protein , 2 types, 3 molecules DFL

#3: Protein Lipoprotein-releasing system ATP-binding protein LolD


Mass: 26306.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminal His-tag (GSHHHHHH) / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lolD, ycfV, b1117, JW5162 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P75957, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate
#4: Protein Major outer membrane lipoprotein Lpp / Braun lipoprotein / BLP / Murein-lipoprotein


Mass: 7691.395 Da / Num. of mol.: 1
Mutation: delta K58 and C-terminal linker-strep II tag LESAWSHPQFEK
Source method: isolated from a genetically manipulated source
Details: Mature form with signal sequence 1-20 removed. / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lpp, mlpA, mulI, b1677, JW1667 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P69776

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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-Z41 / (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate


Mass: 568.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H68O5 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: LolCDE lipoprotein ABC transporter complex with bound lipoprotein LPP
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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: 105000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 47.37 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1Warpparticle selection
9PHENIXmodel refinement
13Warp3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 999999 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingDetails: Composite from PDB entries / Source name: Other / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 130.64 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002710030
ELECTRON MICROSCOPYf_angle_d0.501513566
ELECTRON MICROSCOPYf_chiral_restr0.04091578
ELECTRON MICROSCOPYf_plane_restr0.00321744
ELECTRON MICROSCOPYf_dihedral_angle_d4.92991416

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