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- EMDB-23783: LolCDE nucleotide-free -

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Basic information

Entry
Database: EMDB / ID: EMD-23783
TitleLolCDE nucleotide-free
Map dataCryo-EM map of LolCDE in the nucleotide-free conformation
Sample
  • Complex: Lipo-releasing system transmembrane protein lolC (E.C.3.6.3.-), Lipoprotein-releasing system transmembrane protein (E.C.3.6.3.-), Lipoprotein-releasing system ATP-binding protein LolD (E.C.7.6.2.-), Triacyl-lipoprotein
    • Protein or peptide: Lipoprotein-releasing system transmembrane protein LolC
    • Protein or peptide: Lipoprotein-releasing system transmembrane protein LolE
    • Protein or peptide: Lipoprotein-releasing system ATP-binding protein LolD
  • Protein or peptide: Triacyl-lipoprotein
  • Ligand: PENTADECANOIC ACID
  • Ligand: (2R)-2-(tridecanoyloxy)propyl hexadecanoate
KeywordsATP binding cassette transporter / ABC transporter / inner membrane / protein transport / MEMBRANE PROTEIN
Function / homology
Function and homology information


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 / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space ...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 / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space / ATP hydrolysis 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 / MacB, ATP-binding domain / ABC transporter, lipoprotein release, LolD / ABC3 transporter permease protein domain ...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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Lipoprotein-releasing system transmembrane protein LolC / Lipoprotein-releasing system ATP-binding protein LolD / Lipoprotein-releasing system transmembrane protein LolE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.128
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.128
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7mdx
  • Surface level: 0.128
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23783.png

Downloads & links

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Map

FileDownload / File: emd_23783.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of LolCDE in the nucleotide-free conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 192 pix.
= 203.52 Å		1.06 Å/pix.
x 192 pix.
= 203.52 Å		1.06 Å/pix.
x 192 pix.
= 203.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.128 / Movie #1: 0.128
Minimum - Maximum-1.5076224 - 1.7991339
Average (Standard dev.)-0.00006214968 (±0.05426773)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 203.51999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z203.520203.520203.520
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-1.5081.799-0.000

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Supplemental data

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Sample components

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Entire : Lipo-releasing system transmembrane protein lolC (E.C.3.6.3.-), L...

EntireName: Lipo-releasing system transmembrane protein lolC (E.C.3.6.3.-), Lipoprotein-releasing system transmembrane protein (E.C.3.6.3.-), Lipoprotein-releasing system ATP-binding protein LolD (E.C.7.6. ...Name: Lipo-releasing system transmembrane protein lolC (E.C.3.6.3.-), Lipoprotein-releasing system transmembrane protein (E.C.3.6.3.-), Lipoprotein-releasing system ATP-binding protein LolD (E.C.7.6.2.-), Triacyl-lipoprotein
Components
  • Complex: Lipo-releasing system transmembrane protein lolC (E.C.3.6.3.-), Lipoprotein-releasing system transmembrane protein (E.C.3.6.3.-), Lipoprotein-releasing system ATP-binding protein LolD (E.C.7.6.2.-), Triacyl-lipoprotein
    • Protein or peptide: Lipoprotein-releasing system transmembrane protein LolC
    • Protein or peptide: Lipoprotein-releasing system transmembrane protein LolE
    • Protein or peptide: Lipoprotein-releasing system ATP-binding protein LolD
  • Protein or peptide: Triacyl-lipoprotein
  • Ligand: PENTADECANOIC ACID
  • Ligand: (2R)-2-(tridecanoyloxy)propyl hexadecanoate

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Supramolecule #1: Lipo-releasing system transmembrane protein lolC (E.C.3.6.3.-), L...

SupramoleculeName: Lipo-releasing system transmembrane protein lolC (E.C.3.6.3.-), Lipoprotein-releasing system transmembrane protein (E.C.3.6.3.-), Lipoprotein-releasing system ATP-binding protein LolD (E.C.7.6. ...Name: Lipo-releasing system transmembrane protein lolC (E.C.3.6.3.-), Lipoprotein-releasing system transmembrane protein (E.C.3.6.3.-), Lipoprotein-releasing system ATP-binding protein LolD (E.C.7.6.2.-), Triacyl-lipoprotein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 130 kDa/nm

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Macromolecule #1: Lipoprotein-releasing system transmembrane protein LolC

MacromoleculeName: Lipoprotein-releasing system transmembrane protein LolC
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 42.530609 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: YQPVALFIGL RYMRGRAADR FGRFVSWLST IGITLGVMAL VTVLSVMNGF ERELQNNILG LMPQAILSSE HGSLNPQQLP ETAVKLDGV NRVAPITTGD VVLQSARSVA VGVMLGIDPA QKDPLTPYLV NVKQTDLEPG KYNVILGEQL ASQLGVNRGD Q IRVMVPSA ...String:
YQPVALFIGL RYMRGRAADR FGRFVSWLST IGITLGVMAL VTVLSVMNGF ERELQNNILG LMPQAILSSE HGSLNPQQLP ETAVKLDGV NRVAPITTGD VVLQSARSVA VGVMLGIDPA QKDPLTPYLV NVKQTDLEPG KYNVILGEQL ASQLGVNRGD Q IRVMVPSA SQFTPMGRIP SQRLFNVIGT FAANSEVDGY EMLVNIEDAS RLMRYPAGNI TGWRLWLDEP LKVDSLSQQK LP EGSKWQD WRDRKGELFQ AVRMEKNMMG LLLSLIVAVA AFNIITSLGL MVMEKQGEVA ILQTQGLTPR QIMMVFMVQG ASA GIIGAI LGAALGALLA SQLNNLMPII GVLLDGAALP VAIEPLQVIV IALVAMAIAL LSTLYPSWRA AATQPAE

UniProtKB: Lipoprotein-releasing system transmembrane protein LolC

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Macromolecule #2: Lipoprotein-releasing system transmembrane protein LolE

MacromoleculeName: Lipoprotein-releasing system transmembrane protein LolE
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 44.200496 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SLLIGLRFSR GRRRGGMVSL ISVISTIGIA LGVAVLIVGL SAMNGFEREL NNRILAVVPH GEIEAVDQPW TNWQEALDHV QKVPGIAAA APYINFTGLV ESGANLRAIQ VKGVNPQQEQ RLSALPSFVQ GDAWRNFKAG EQQIIIGKGV ADALKVKQGD W VSIMIPNS ...String:
SLLIGLRFSR GRRRGGMVSL ISVISTIGIA LGVAVLIVGL SAMNGFEREL NNRILAVVPH GEIEAVDQPW TNWQEALDHV QKVPGIAAA APYINFTGLV ESGANLRAIQ VKGVNPQQEQ RLSALPSFVQ GDAWRNFKAG EQQIIIGKGV ADALKVKQGD W VSIMIPNS NPEHKLMQPK RVRLHVAGIL QLSGQLDHSF AMIPLADAQQ YLDMGSSVSG IALKMTDVFN ANKLVRDAGE VT NSYVYIK SWIGTYGYMY RDIQMIRAIM YLAMVLVIGV ACFNIVSTLV MAVKDKSGDI AVLRTLGAKD GLIRAIFVWY GLL AGLFGS LCGVIIGVVV SLQLTPIIEW IEKLIGHQFL SSDIYFIDFL PSELHWLDVF YVLVTALLLS LLASWYPARR ASNI DPA

UniProtKB: Lipoprotein-releasing system transmembrane protein LolE

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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: 23.823326 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ILLQCDNLCK RYQEGSVQTD VLHNVSFSVG EGEMMAIVGS SGSGKSTLLH LLGGLDTPTS GDVIFNGQPM SKLSSAAKAE LRNQKLGFI YQFHHLLPDF TALENVAMPL LIGKKKPAEI NSRALEMLKA VGLDHRANHR PSELSGGERQ RVAIARALVN N PRLVLADE ...String:
ILLQCDNLCK RYQEGSVQTD VLHNVSFSVG EGEMMAIVGS SGSGKSTLLH LLGGLDTPTS GDVIFNGQPM SKLSSAAKAE LRNQKLGFI YQFHHLLPDF TALENVAMPL LIGKKKPAEI NSRALEMLKA VGLDHRANHR PSELSGGERQ RVAIARALVN N PRLVLADE PTGNLDARNA DSIFQLLGEL NRLQGTAFLV VTHDLQLAKR MSRQLEMRDG

UniProtKB: Lipoprotein-releasing system ATP-binding protein LolD

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Macromolecule #4: Triacyl-lipoprotein

MacromoleculeName: Triacyl-lipoprotein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 492.547 Da
SequenceString:
(DCY)(DSN)(DAL)(DAL)AA

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Macromolecule #5: PENTADECANOIC ACID

MacromoleculeName: PENTADECANOIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: F15
Molecular weightTheoretical: 242.397 Da
Chemical component information

ChemComp-F15:
PENTADECANOIC ACID

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Macromolecule #6: (2R)-2-(tridecanoyloxy)propyl hexadecanoate

MacromoleculeName: (2R)-2-(tridecanoyloxy)propyl hexadecanoate / type: ligand / ID: 6 / Number of copies: 1 / Formula: ZM5
Molecular weightTheoretical: 526.832 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

Concentration1.6 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 46.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104875
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)

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