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- PDB-9rlh: LolCDE complex with del 9-15 LolB lipoprotein -

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Basic information

Entry
Database: PDB / ID: 9rlh
TitleLolCDE complex with del 9-15 LolB lipoprotein
Components
  • (Lipoprotein-releasing system transmembrane protein ...) x 2
  • Lipoprotein-releasing system ATP-binding protein LolD
  • Outer-membrane lipoprotein LolB
KeywordsPROTEIN TRANSPORT / Gram-negative / envelope biogenesis / outer membrane protein
Function / homology
Function and homology information


lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / lipoprotein metabolic process / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / lipoprotein transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / cell outer membrane ...lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / lipoprotein metabolic process / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / lipoprotein transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / cell outer membrane / transmembrane transport / protein transport / outer membrane-bounded periplasmic space / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Outer membrane lipoprotein LolB / Outer membrane lipoprotein LolB / Lipoprotein localisation LolA/LolB/LppX / 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 ...Outer membrane lipoprotein LolB / Outer membrane lipoprotein LolB / Lipoprotein localisation LolA/LolB/LppX / 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 / Outer-membrane lipoprotein LolB / 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: 3.19 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: To Be Published
Title: LolCDE complex with del 9-15 LolB lipoprotein
Authors: Symmons, M.F. / Szewczyk, P. / Greene, N.P. / Hardwick, S.W. / Koronakis, V.
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: 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
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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: Outer-membrane lipoprotein LolB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,8987
Polymers164,0725
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(DE3) (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(DE3) (bacteria) / References: UniProt: P75958

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Protein , 2 types, 3 molecules DFL

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


Mass: 26444.301 Da / Num. of mol.: 2 / Mutation: C-terminal His tag (GSHHHHHH)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lolD, ycfV, b1117, JW5162 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P75957, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate
#4: Protein Outer-membrane lipoprotein LolB


Mass: 22502.213 Da / Num. of mol.: 1 / Mutation: delta 9-15 C-terminal alfa tag
Source method: isolated from a genetically manipulated source
Details: chain is delta 9-15 in mature form of protein with 1-21 in Uniprot sequence removed in mature form.
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: lolB, hemM, ychC, b1209, JW1200 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61320

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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 del 9-15 lipoprotein LolB
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
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: 130000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 52.79 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1Warpparticle selection
7Cootmodel fitting
9PHENIXmodel refinement
13Warp3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168742 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingDetails: previously refined Lpp (L10P) complex / Source name: Other / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 131.9 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003910033
ELECTRON MICROSCOPYf_angle_d0.603413571
ELECTRON MICROSCOPYf_chiral_restr0.04341574
ELECTRON MICROSCOPYf_plane_restr0.00351744
ELECTRON MICROSCOPYf_dihedral_angle_d4.95891415

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