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- EMDB-23784: LolCDE nucleotide-free -

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Basic information

Entry
Database: EMDB / ID: EMD-23784
TitleLolCDE nucleotide-free
Map dataCryo-EM map of LolCDE in the nucleotide-bound conformation
Sample
  • Complex: Complex of LolC, LolE and LolD in a 1:1:2 stoichiometry
    • Protein or peptide: Lipoprotein transporter subunit LolE
    • Protein or peptide: Lipo-releasing system transmembrane protein lolC
  • Protein or peptide: Lipoprotein-releasing system ATP-binding protein LolD
  • Ligand: ADP ORTHOVANADATE
  • Ligand: MAGNESIUM ION
KeywordsATP binding cassette transporter / ABC transporter / inner membrane / transport protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


lipoprotein localization to membrane / lipoprotein releasing activity / lipoprotein localization to outer membrane / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / lipoprotein transport / ATPase-coupled transmembrane transporter activity / membrane => GO:0016020 / hydrolase activity / ATP binding / plasma membrane
Similarity search - Function
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 / ABC3 transporter permease protein domain / FtsX-like permease family / ABC transporter-like, conserved site ...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 / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Lipoprotein-releasing system ATP-binding protein LolD / Lipoprotein-releasing ABC transporter permease subunit LolC / Lipoprotein transporter subunit LolE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSharma S / Liao M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2021
Title: Mechanism of LolCDE as a molecular extruder of bacterial triacylated lipoproteins.
Authors: Stuti Sharma / Ruoyu Zhou / Li Wan / Shan Feng / KangKang Song / Chen Xu / Yanyan Li / Maofu Liao /
Abstract: Lipoproteins are important for bacterial growth and antibiotic resistance. These proteins use lipid acyl chains attached to the N-terminal cysteine residue to anchor on the outer surface of ...Lipoproteins are important for bacterial growth and antibiotic resistance. These proteins use lipid acyl chains attached to the N-terminal cysteine residue to anchor on the outer surface of cytoplasmic membrane. In Gram-negative bacteria, many lipoproteins are transported to the outer membrane (OM), a process dependent on the ATP-binding cassette (ABC) transporter LolCDE which extracts the OM-targeted lipoproteins from the cytoplasmic membrane. Lipid-anchored proteins pose a unique challenge for transport machinery as they have both hydrophobic lipid moieties and soluble protein component, and the underlying mechanism is poorly understood. Here we determined the cryo-EM structures of nanodisc-embedded LolCDE in the nucleotide-free and nucleotide-bound states at 3.8-Å and 3.5-Å resolution, respectively. The structural analyses, together with biochemical and mutagenesis studies, uncover how LolCDE recognizes its substrate by interacting with the lipid and N-terminal peptide moieties of the lipoprotein, and identify the amide-linked acyl chain as the key element for LolCDE interaction. Upon nucleotide binding, the transmembrane helices and the periplasmic domains of LolCDE undergo large-scale, asymmetric movements, resulting in extrusion of the captured lipoprotein. Comparison of LolCDE and MacB reveals the conserved mechanism of type VII ABC transporters and emphasizes the unique properties of LolCDE as a molecule extruder of triacylated lipoproteins.
History
DepositionApr 6, 2021-
Header (metadata) releaseAug 11, 2021-
Map releaseAug 11, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0319
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0319
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7mdy
  • Surface level: 0.0319
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23784.png

Downloads & links

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Map

FileDownload / File: emd_23784.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of LolCDE in the nucleotide-bound conformation
Voxel sizeX=Y=Z: 1.087 Å
Density
Contour LevelBy AUTHOR: 0.0319 / Movie #1: 0.0319
Minimum - Maximum-0.09364155 - 0.16934673
Average (Standard dev.)0.00017902734 (±0.0067948545)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 208.70401 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0871.0871.087
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z208.704208.704208.704
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0940.1690.000

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Supplemental data

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Sample components

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Entire : Complex of LolC, LolE and LolD in a 1:1:2 stoichiometry

EntireName: Complex of LolC, LolE and LolD in a 1:1:2 stoichiometry
Components
  • Complex: Complex of LolC, LolE and LolD in a 1:1:2 stoichiometry
    • Protein or peptide: Lipoprotein transporter subunit LolE
    • Protein or peptide: Lipo-releasing system transmembrane protein lolC
  • Protein or peptide: Lipoprotein-releasing system ATP-binding protein LolD
  • Ligand: ADP ORTHOVANADATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complex of LolC, LolE and LolD in a 1:1:2 stoichiometry

SupramoleculeName: Complex of LolC, LolE and LolD in a 1:1:2 stoichiometry
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 130 kDa/nm

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Macromolecule #1: Lipoprotein transporter subunit LolE

MacromoleculeName: Lipoprotein transporter subunit LolE / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 45.385977 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAMPLSLLIG LRFSRGRRRG GMVSLISVIS TIGIALGVAV LIVGLSAMNG FERELNNRIL AVVPHGEIEA VDQPWTNWQE ALDHVQKVP GIAAAAPYIN FTGLVESGAN LRAIQVKGVN PQQEQRLSAL PSFVQGDAWR NFKAGEQQII IGKGVADALK V KQGDWVSI ...String:
MAMPLSLLIG LRFSRGRRRG GMVSLISVIS TIGIALGVAV LIVGLSAMNG FERELNNRIL AVVPHGEIEA VDQPWTNWQE ALDHVQKVP GIAAAAPYIN FTGLVESGAN LRAIQVKGVN PQQEQRLSAL PSFVQGDAWR NFKAGEQQII IGKGVADALK V KQGDWVSI MIPNSNPEHK LMQPKRVRLH VAGILQLSGQ LDHSFAMIPL ADAQQYLDMG SSVSGIALKM TDVFNANKLV RD AGEVTNS YVYIKSWIGT YGYMYRDIQM IRAIMYLAMV LVIGVACFNI VSTLVMAVKD KSGDIAVLRT LGAKDGLIRA IFV WYGLLA GLFGSLCGVI IGVVVSLQLT PIIEWIEKLI GHQFLSSDIY FIDFLPSELH WLDVFYVLVT ALLLSLLASW YPAR RASNI DPARVLSGQ

UniProtKB: Lipoprotein transporter subunit LolE

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Macromolecule #2: Lipo-releasing system transmembrane protein lolC

MacromoleculeName: Lipo-releasing system transmembrane protein lolC / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 43.295516 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYQPVALFIG LRYMRGRAAD RFGRFVSWLS TIGITLGVMA LVTVLSVMNG FERELQNNIL GLMPQAILSS EHGSLNPQQL PETAVKLDG VNRVAPITTG DVVLQSARSV AVGVMLGIDP AQKDPLTPYL VNVKQTDLEP GKYNVILGEQ LASQLGVNRG D QIRVMVPS ...String:
MYQPVALFIG LRYMRGRAAD RFGRFVSWLS TIGITLGVMA LVTVLSVMNG FERELQNNIL GLMPQAILSS EHGSLNPQQL PETAVKLDG VNRVAPITTG DVVLQSARSV AVGVMLGIDP AQKDPLTPYL VNVKQTDLEP GKYNVILGEQ LASQLGVNRG D QIRVMVPS ASQFTPMGRI PSQRLFNVIG TFAANSEVDG YEMLVNIEDA SRLMRYPAGN ITGWRLWLDE PLKVDSLSQQ KL PEGSKWQ DWRDRKGELF QAVRMEKNMM GLLLSLIVAV AAFNIITSLG LMVMEKQGEV AILQTQGLTP RQIMMVFMVQ GAS AGIIGA ILGAALGALL ASQLNNLMPI IGVLLDGAAL PVAIEPLQVI VIALVAMAIA LLSTLYPSWR AAATQPAEAL RYE

UniProtKB: Lipoprotein-releasing ABC transporter permease subunit LolC

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

MacromoleculeName: Lipoprotein-releasing system ATP-binding protein LolD / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 25.815721 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KILLQCDNLC KRYQEGSVQT DVLHNVSFSV GEGEMMAIVG SSGSGKSTLL HLLGGLDTPT SGDVIFNGQP MSKLSSAAKA ELRNQKLGF IYQFHHLLPD FTALENVAMP LLIGKKKPAE INSRALEMLK AVGLDHRANH RPSELSGGER QRVAIARALV N NPRLVLAD ...String:
KILLQCDNLC KRYQEGSVQT DVLHNVSFSV GEGEMMAIVG SSGSGKSTLL HLLGGLDTPT SGDVIFNGQP MSKLSSAAKA ELRNQKLGF IYQFHHLLPD FTALENVAMP LLIGKKKPAE INSRALEMLK AVGLDHRANH RPSELSGGER QRVAIARALV N NPRLVLAD EPTGNLDARN ADSIFQLLGE LNRLQGTAFL VVTHDLQLAK RMSRQLEMRD GRLTAELSMG RLTAELSM

UniProtKB: Lipoprotein-releasing system ATP-binding protein LolD

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Macromolecule #4: ADP ORTHOVANADATE

MacromoleculeName: ADP ORTHOVANADATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: AOV
Molecular weightTheoretical: 544.156 Da
Chemical component information

ChemComp-AOV:
ADP ORTHOVANADATE / energy-carrying molecule analogue*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31971
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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