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- PDB-7v8l: LolCDE with bound RcsF in nanodiscs -

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Basic information

Entry
Database: PDB / ID: 7v8l
TitleLolCDE with bound RcsF in nanodiscs
Components
  • Lipoprotein-releasing system ATP-binding protein LolD
  • Lipoprotein-releasing system transmembrane protein LolC
  • Lipoprotein-releasing system transmembrane protein LolE
  • Outer membrane lipoprotein RcsF
KeywordsMEMBRANE PROTEIN / ABC transporter / lipoprotein
Function / homology
Function and homology information


positive regulation of phosphorelay signal transduction system / periplasmic side of cell outer membrane / outer membrane protein complex / lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / lipoprotein transport / cellular response to cell envelope stress ...positive regulation of phosphorelay signal transduction system / periplasmic side of cell outer membrane / outer membrane protein complex / lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / plasma membrane protein complex / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / lipoprotein transport / cellular response to cell envelope stress / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / cell outer membrane / transmembrane transport / outer membrane-bounded periplasmic space / intracellular signal transduction / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Outer membrane lipoprotein RcsF / RcsF lipoprotein / 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 / MacB, ATP-binding domain / ABC transporter, lipoprotein release, LolD ...Outer membrane lipoprotein RcsF / RcsF lipoprotein / 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 / MacB, ATP-binding domain / ABC transporter, lipoprotein release, LolD / ABC3 transporter permease protein domain / FtsX-like permease family / 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
Chem-PCJ / Lipoprotein-releasing system transmembrane protein LolC / Outer membrane lipoprotein RcsF / 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: 3.5 Å
AuthorsBei, W.W. / Luo, Q.S. / Shi, H.G. / Zhang, X.Z. / Huang, Y.H.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0500404 China
Chinese Academy of SciencesXDB37020201 China
National Natural Science Foundation of China (NSFC)31625009 China
CitationJournal: PLoS Biol / Year: 2022
Title: Cryo-EM structures of LolCDE reveal the molecular mechanism of bacterial lipoprotein sorting in Escherichia coli.
Authors: Weiwei Bei / Qingshan Luo / Huigang Shi / Haizhen Zhou / Min Zhou / Xinzheng Zhang / Yihua Huang /
Abstract: Bacterial lipoproteins perform a diverse array of functions including bacterial envelope biogenesis and microbe-host interactions. Lipoproteins in gram-negative bacteria are sorted to the outer ...Bacterial lipoproteins perform a diverse array of functions including bacterial envelope biogenesis and microbe-host interactions. Lipoproteins in gram-negative bacteria are sorted to the outer membrane (OM) via the localization of lipoproteins (Lol) export pathway. The ATP-binding cassette (ABC) transporter LolCDE initiates the Lol pathway by selectively extracting and transporting lipoproteins for trafficking. Here, we report cryo-EM structures of LolCDE in apo, lipoprotein-bound, and AMPPNP-bound states at a resolution of 3.5 to 4.2 Å. Structure-based disulfide crosslinking, photo-crosslinking, and functional complementation assay verify the apo-state structure and reveal the molecular details regarding substrate selectivity and substrate entry route. Our studies snapshot 3 functional states of LolCDE in a transport cycle, providing deep insights into the mechanisms that underlie LolCDE-mediated lipoprotein sorting in E. coli.
History
DepositionAug 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Lipoprotein-releasing system transmembrane protein LolE
A: Outer membrane lipoprotein RcsF
C: Lipoprotein-releasing system transmembrane protein LolC
D: Lipoprotein-releasing system ATP-binding protein LolD
F: Lipoprotein-releasing system ATP-binding protein LolD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,0276
Polymers152,1305
Non-polymers8961
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: 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) / Strain: K-12 / Gene: lolE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P75958
#2: Protein Outer membrane lipoprotein RcsF


Mass: 12506.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rcsF / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P69411
#3: 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) / Strain: K-12 / Gene: lolC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0ADC3
#4: Protein Lipoprotein-releasing system ATP-binding protein LolD


Mass: 25471.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: lolD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P75957, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate
#5: Chemical ChemComp-PCJ / (2R)-3-{[(2S)-3-HYDROXY-2-(PALMITOYLAMINO)PROPYL]THIO}PROPANE-1,2-DIYL DIHEXADECANOATE


Mass: 896.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C54H105NO6S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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-RcsF complex in nanodiscs / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: NITROGEN / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2200 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 225933 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029492
ELECTRON MICROSCOPYf_angle_d0.57512901
ELECTRON MICROSCOPYf_dihedral_angle_d4.0431335
ELECTRON MICROSCOPYf_chiral_restr0.0431541
ELECTRON MICROSCOPYf_plane_restr0.0061664

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