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- EMDB-35252: Density map of the OmpC3-MlaA2 complex in MSP2N2 nanodiscs disulf... -

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Basic information

Entry
Database: EMDB / ID: EMD-35252
TitleDensity map of the OmpC3-MlaA2 complex in MSP2N2 nanodiscs disulfide-bonded to MlaC
Map data
Sample
  • Complex: OmpC3-MlaA2 complex in MSP2N2 nanodiscs disulfide-bonded to MlaC
    • Complex: Outer membrane porin C
    • Complex: Complex of MlaA disulfide trapped with MlaC
Keywordsbacteria / outer membrane / phospholipid / lipid asymmetry / membrane protein / protein complex structure / channel / LIPID TRANSPORT
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsYeow J / Luo M / Chng SS
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Other governmentMOH-000145 Singapore
CitationJournal: Nat Commun / Year: 2023
Title: Molecular mechanism of phospholipid transport at the bacterial outer membrane interface.
Authors: Jiang Yeow / Min Luo / Shu-Sin Chng /
Abstract: The outer membrane (OM) of Gram-negative bacteria is an asymmetric lipid bilayer with outer leaflet lipopolysaccharides and inner leaflet phospholipids (PLs). This unique lipid asymmetry renders the ...The outer membrane (OM) of Gram-negative bacteria is an asymmetric lipid bilayer with outer leaflet lipopolysaccharides and inner leaflet phospholipids (PLs). This unique lipid asymmetry renders the OM impermeable to external insults, including antibiotics and bile salts. To maintain this barrier, the OmpC-Mla system removes mislocalized PLs from the OM outer leaflet, and transports them to the inner membrane (IM); in the first step, the OmpC-MlaA complex transfers PLs to the periplasmic chaperone MlaC, but mechanistic details are lacking. Here, we biochemically and structurally characterize the MlaA-MlaC transient complex. We map the interaction surfaces between MlaA and MlaC in Escherichia coli, and show that electrostatic interactions are important for MlaC recruitment to the OM. We further demonstrate that interactions with MlaC modulate conformational states in MlaA. Finally, we solve a 2.9-Å cryo-EM structure of a disulfide-trapped OmpC-MlaA-MlaC complex in nanodiscs, reinforcing the mechanism of MlaC recruitment, and highlighting membrane thinning as a plausible strategy for directing lipids for transport. Our work offers critical insights into retrograde PL transport by the OmpC-Mla system in maintaining OM lipid asymmetry.
History
DepositionFeb 5, 2023-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateDec 27, 2023-
Current statusDec 27, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35252.png

Downloads & links

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Map

FileDownload / File: emd_35252.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 266.88 Å		0.83 Å/pix.
x 320 pix.
= 266.88 Å		0.83 Å/pix.
x 320 pix.
= 266.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.19202083 - 0.5035111
Average (Standard dev.)0.004927592 (±0.01844426)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_35252_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35252_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35252_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : OmpC3-MlaA2 complex in MSP2N2 nanodiscs disulfide-bonded to MlaC

EntireName: OmpC3-MlaA2 complex in MSP2N2 nanodiscs disulfide-bonded to MlaC
Components
  • Complex: OmpC3-MlaA2 complex in MSP2N2 nanodiscs disulfide-bonded to MlaC
    • Complex: Outer membrane porin C
    • Complex: Complex of MlaA disulfide trapped with MlaC

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Supramolecule #1: OmpC3-MlaA2 complex in MSP2N2 nanodiscs disulfide-bonded to MlaC

SupramoleculeName: OmpC3-MlaA2 complex in MSP2N2 nanodiscs disulfide-bonded to MlaC
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Outer membrane complex of 3OmpC with disulfide-trapped 2MlaA and 2MlaC reconstituted in Escherichia coli polar lipids and MSP2N2 nanodiscs
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12 / Location in cell: Outer membrane
Molecular weightTheoretical: 52 KDa

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Supramolecule #2: Outer membrane porin C

SupramoleculeName: Outer membrane porin C / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: Trimeric OmpC porins in complex with MlaA at the outer membrane disulfide-trapped with MlaC
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12 / Location in cell: Outer membrane

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Supramolecule #3: Complex of MlaA disulfide trapped with MlaC

SupramoleculeName: Complex of MlaA disulfide trapped with MlaC / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Details: Intermembrane phospholipid transport system lipoprotein MlaA disulfide trapped with MlaC

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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

Concentration12 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClsodium chloride

Details: Tris-buffered saline (TBS) buffer (20 mM Tris HCl pH 8.0, 150 mM NaCl)
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Tridiem 4K / Energy filter - Slit width: 20 eV
Details: Gatan GIF post-column energy filter operated in zero-loss mode
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 6018 / Average exposure time: 5.99 sec. / Average electron dose: 90.0 e/Å2
Details: Images were collected in movie-mode at 50 frames per image
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2434319
Details: We performed automated particle picking using Blob and Template Picker for initial template picking and final sampling respectively.
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0.0) / Number images used: 90496
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0.0)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.0.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Overall B value: 73.8

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