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- EMDB-11931: Subtomogram average of outer membrane dome protein (OMDP)-C8 symm... -

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Basic information

Entry
Database: EMDB / ID: EMD-11931
TitleSubtomogram average of outer membrane dome protein (OMDP)-C8 symmetrized
Map dataSTA of Outer membrane protein complexed-C8 symmetrized
Sample
  • Organelle or cellular component: Subtomogram average of outer membrane dome protein (OMDP)-C8 symmetrized
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 40.2 Å
AuthorsKlein S / Wimmer B / Winter S / Kolovou A / Laketa V / Chlanda P
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1129 P19 Germany
Citation
Journal: Commun Biol / Year: 2021
Title: Post-correlation on-lamella cryo-CLEM reveals the membrane architecture of lamellar bodies.
Authors: Steffen Klein / Benedikt H Wimmer / Sophie L Winter / Androniki Kolovou / Vibor Laketa / Petr Chlanda /
Abstract: Lamellar bodies (LBs) are surfactant-rich organelles in alveolar cells. LBs disassemble into a lipid-protein network that reduces surface tension and facilitates gas exchange in the alveolar cavity. ...Lamellar bodies (LBs) are surfactant-rich organelles in alveolar cells. LBs disassemble into a lipid-protein network that reduces surface tension and facilitates gas exchange in the alveolar cavity. Current knowledge of LB architecture is predominantly based on electron microscopy studies using disruptive sample preparation methods. We established and validated a post-correlation on-lamella cryo-correlative light and electron microscopy approach for cryo-FIB milled cells to structurally characterize and validate the identity of LBs in their unperturbed state. Using deconvolution and 3D image registration, we were able to identify fluorescently labeled membrane structures analyzed by cryo-electron tomography. In situ cryo-electron tomography of A549 cells as well as primary Human Small Airway Epithelial Cells revealed that LBs are composed of membrane sheets frequently attached to the limiting membrane through "T"-junctions. We report a so far undescribed outer membrane dome protein complex (OMDP) on the limiting membrane of LBs. Our data suggest that LB biogenesis is driven by parallel membrane sheet import and by the curvature of the limiting membrane to maximize lipid storage capacity.
#1: Journal: Biorxiv / Year: 2020
Title: Post-correlation on-lamella cryo-CLEM reveals the membrane architecture of lamellar bodies
Authors: Klein S / Wimmer BH / Winter SL / Kolovou A / Lakota V / Chlanda P
History
DepositionNov 9, 2020-
Header (metadata) releaseNov 18, 2020-
Map releaseNov 18, 2020-
UpdateFeb 10, 2021-
Current statusFeb 10, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.712
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.712
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11931.png

Downloads & links

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Map

FileDownload / File: emd_11931.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSTA of Outer membrane protein complexed-C8 symmetrized
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.3 Å/pix.
x 100 pix.
= 430.2 Å		4.3 Å/pix.
x 100 pix.
= 430.2 Å		4.3 Å/pix.
x 100 pix.
= 430.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.302 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.712 / Movie #1: 0.712
Minimum - Maximum-3.4081357 - 3.035075
Average (Standard dev.)-0.5341212 (±0.91052055)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 430.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.3024.3024.302
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z430.200430.200430.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-3.4083.035-0.534

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Supplemental data

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Half map: odd map

Fileemd_11931_half_map_1.map
Annotationodd map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: even map

Fileemd_11931_half_map_2.map
Annotationeven 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 : Subtomogram average of outer membrane dome protein (OMDP)-C8 symm...

EntireName: Subtomogram average of outer membrane dome protein (OMDP)-C8 symmetrized
Components
  • Organelle or cellular component: Subtomogram average of outer membrane dome protein (OMDP)-C8 symmetrized

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Supramolecule #1: Subtomogram average of outer membrane dome protein (OMDP)-C8 symm...

SupramoleculeName: Subtomogram average of outer membrane dome protein (OMDP)-C8 symmetrized
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: A549 human lung cell line
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE
DetailsA549 cell line

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus min: 4.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C8 (8 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 40.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: IMOD / Number subtomograms used: 116
ExtractionNumber tomograms: 2 / Number images used: 116 / Software - Name: Dynamo
CTF correctionSoftware - Name: IMOD
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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