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- EMDB-36823: DDM-bound complex of OmpC3-MlaA-MlaC -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-36823
TitleDDM-bound complex of OmpC3-MlaA-MlaC
Map dataFull map of DDM-bound complex of OmpC3-MlaA-MlaC
Sample
  • Complex: DDM-bound outer membrane complex of OmpC-MlaA with periplasmic MlaC
    • Complex: Outer membrane porin C
    • Complex: Intermembrane phospholipid transport system lipoprotein MlaA
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: 3.5 Å
AuthorsYeow J / Luo M / Chng SS
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Other governmentMOH-000145 Singapore
CitationJournal: To Be Published
Title: Molecular mechanism of phospholipid transport at the bacterial outer membrane interface
Authors: Yeow J / Luo M / Chng SS
History
DepositionJul 12, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36823.png

Downloads & links

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Map

FileDownload / File: emd_36823.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map of DDM-bound complex of OmpC3-MlaA-MlaC
Voxel sizeX=Y=Z: 0.834 Å
Density
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.19630608 - 0.3744454
Average (Standard dev.)0.0018860555 (±0.0138738295)
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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Half map: Half map B of DDM-bound complex of OmpC3-MlaA-MlaC

Fileemd_36823_half_map_1.map
AnnotationHalf map B of DDM-bound complex of OmpC3-MlaA-MlaC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of DDM-bound complex of OmpC3-MlaA-MlaC

Fileemd_36823_half_map_2.map
AnnotationHalf map A of DDM-bound complex of OmpC3-MlaA-MlaC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DDM-bound outer membrane complex of OmpC-MlaA with periplasmic MlaC

EntireName: DDM-bound outer membrane complex of OmpC-MlaA with periplasmic MlaC
Components
  • Complex: DDM-bound outer membrane complex of OmpC-MlaA with periplasmic MlaC
    • Complex: Outer membrane porin C
    • Complex: Intermembrane phospholipid transport system lipoprotein MlaA

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Supramolecule #1: DDM-bound outer membrane complex of OmpC-MlaA with periplasmic MlaC

SupramoleculeName: DDM-bound outer membrane complex of OmpC-MlaA with periplasmic MlaC
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: DDM-bound outer membrane complex of OmpC with disulfide-trapped MlaA and MlaC
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12
Molecular weightTheoretical: 28 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: OmpC
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12

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Supramolecule #3: Intermembrane phospholipid transport system lipoprotein MlaA

SupramoleculeName: Intermembrane phospholipid transport system lipoprotein MlaA
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: MlaA

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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)
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: 5816 / 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: 402090
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 reconstructionNumber classes used: 37 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0.0) / Number images used: 27443
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 classificationSoftware - Name: cryoSPARC (ver. 4.0.0)
FSC plot (resolution estimation)

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