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- EMDB-11882: LolCDE in complex with lipoprotein -

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Basic information

Entry
Database: EMDB / ID: EMD-11882
TitleLolCDE in complex with lipoprotein
Map data
SampleLolCDE in complex with a lipoprotein
  • Lipoprotein-releasing ABC transporter permease subunit LolC
  • (Lipoprotein-releasing system ...) x 2
  • LPP
  • (ligand) x 2
Function / homology
Function and homology information


lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / plasma membrane protein complex / lipoprotein transport / transmembrane transporter activity / transmembrane transport / ATPase / integral component of plasma membrane ...lipoprotein releasing activity / protein localization to outer membrane / lipoprotein localization to outer membrane / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / plasma membrane protein complex / lipoprotein transport / transmembrane transporter activity / transmembrane transport / ATPase / integral component of plasma membrane / integral component of membrane / ATP binding / plasma membrane
ABC transporter-like / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / MacB-like periplasmic core domain / ABC transporter, conserved site / ABC transporter, lipoprotein release, LolD / Lipoprotein-releasing system transmembrane protein LolE, gammaproteobacteria type / Lipoprotein-releasing system transmembrane protein LolC/E / Lipoprotein releasing system, ATP-binding protein / ABC3 transporter permease protein domain
Lipoprotein-releasing ABC transporter permease subunit LolC / Lipoprotein-releasing system ATP-binding protein LolD / Lipoprotein-releasing system transmembrane protein LolE
Biological speciesEscherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsTang XD / Chang SH / Zhang K / Wang T / Luo QH / Qiao W / Wang C / Zhang ZB / Zhang ZY / Zhu XF ...Tang XD / Chang SH / Zhang K / Wang T / Luo QH / Qiao W / Wang C / Zhang ZB / Zhang ZY / Zhu XF / Dong CJ / Zhang X / Dong HH
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Structural basis for bacterial lipoprotein relocation by the transporter LolCDE.
Authors: Xiaodi Tang / Shenghai Chang / Ke Zhang / Qinghua Luo / Zhengyu Zhang / Ting Wang / Wen Qiao / Chen Wang / Chongrong Shen / Zhibo Zhang / Xiaofeng Zhu / Xiawei Wei / Changjiang Dong / Xing ...Authors: Xiaodi Tang / Shenghai Chang / Ke Zhang / Qinghua Luo / Zhengyu Zhang / Ting Wang / Wen Qiao / Chen Wang / Chongrong Shen / Zhibo Zhang / Xiaofeng Zhu / Xiawei Wei / Changjiang Dong / Xing Zhang / Haohao Dong /
Abstract: Lipoproteins in the outer membrane of Gram-negative bacteria are involved in various vital physiological activities, including multidrug resistance. Synthesized in the cytoplasm and matured in the ...Lipoproteins in the outer membrane of Gram-negative bacteria are involved in various vital physiological activities, including multidrug resistance. Synthesized in the cytoplasm and matured in the inner membrane, lipoproteins must be transported to the outer membrane through the Lol pathway mediated by the ATP-binding cassette transporter LolCDE in the inner membrane via an unknown mechanism. Here, we report cryo-EM structures of Escherichia coli LolCDE in apo, lipoprotein-bound, LolA-bound, ADP-bound and AMP-PNP-bound states at a resolution of 3.2-3.8 Å, covering the complete lipoprotein transport cycle. Mutagenesis and in vivo viability assays verify features of the structures and reveal functional residues and structural characteristics of LolCDE. The results provide insights into the mechanisms of sorting and transport of outer-membrane lipoproteins and may guide the development of novel therapies against multidrug-resistant Gram-negative bacteria.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionOct 25, 2020-
Header (metadata) releaseApr 7, 2021-
Map releaseApr 7, 2021-
UpdateApr 28, 2021-
Current statusApr 28, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7arh
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11882.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 240 pix.
= 243.36 Å
1.01 Å/pix.
x 240 pix.
= 243.36 Å
1.01 Å/pix.
x 240 pix.
= 243.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.022
Minimum - Maximum-0.07418705 - 0.1302935
Average (Standard dev.)-0.00012081613 (±0.00384513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 243.36002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z243.360243.360243.360
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0740.130-0.000

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Supplemental data

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Sample components

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Entire LolCDE in complex with a lipoprotein

EntireName: LolCDE in complex with a lipoprotein / Number of components: 7

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Component #1: protein, LolCDE in complex with a lipoprotein

ProteinName: LolCDE in complex with a lipoprotein / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli) / Strain: K12
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pTRC99a / Strain: C43

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Component #2: protein, Lipoprotein-releasing ABC transporter permease subunit LolC

ProteinName: Lipoprotein-releasing ABC transporter permease subunit LolC
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.295516 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #3: protein, Lipoprotein-releasing system transmembrane protein LolE

ProteinName: Lipoprotein-releasing system transmembrane protein LolE
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.385977 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #4: protein, Lipoprotein-releasing system ATP-binding protein LolD

ProteinName: Lipoprotein-releasing system ATP-binding protein LolD / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 26.576465 kDa
SourceSpecies: Escherichia coli (strain K12) (bacteria) / Strain: K12
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #5: protein, LPP

ProteinName: LPP / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.079206 kDa
SourceSpecies: Escherichia coli K-12 (bacteria)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #6: ligand, (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate

LigandName: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.568911 kDa

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Component #7: ligand, PALMITIC ACID

LigandName: PALMITIC ACID / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.256424 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 4 mg/mL
Buffer solution: 20 mM Tris-HCl, pH 7.8, 150 mM NaCl and 0.05% LMNG
pH: 7.8
VitrificationCryogen name: ETHANE / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 49517
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Input PDB model: 5NAA, 5UDF, 2PCL, 2PCL
Chain ID: C, E, D, F
Output model

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