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- EMDB-10820: Tomogram of lamellar body (A549 cell expressing ABCA3-eGFP) -

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Basic information

Entry
Database: EMDB / ID: EMD-10820
TitleTomogram of lamellar body (A549 cell expressing ABCA3-eGFP)
Map data
Sample
  • Organelle or cellular component: Lamellar body in A549 cells expressing ABCA3-eGFP
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsKlein S / Wimmer B / Winter S / Kolovou A / Laketa W / Chlanda P
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: 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.
History
DepositionApr 3, 2020-
Header (metadata) releaseFeb 17, 2021-
Map releaseFeb 17, 2021-
UpdateMar 8, 2023-
Current statusMar 8, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Supplemental images

emd_10820.png

Downloads & links

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Map

FileDownload / File: emd_10820.map.gz / Format: CCP4 / Size: 388.4 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.07 Å/pix.
x 94 pix.
= 946.58 Å		10.07 Å/pix.
x 1674 pix.
= 16857.18 Å		10.07 Å/pix.
x 1294 pix.
= 13030.58 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 10.07 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-141.0 - 56.0
Average (Standard dev.)5.074853 (±5.8941636)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin176-2784
Dimensions1674129494
Spacing1294167494
CellA: 13030.58 Å / B: 16857.18 Å / C: 946.57996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z10.0710.0710.07
M x/y/z1294167494
origin x/y/z0.0000.0000.000
length x/y/z13030.58016857.180946.580
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-2781764
NC/NR/NS1294167494
D min/max/mean-141.00056.0005.075

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Supplemental data

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Sample components

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Entire : Lamellar body in A549 cells expressing ABCA3-eGFP

EntireName: Lamellar body in A549 cells expressing ABCA3-eGFP
Components
  • Organelle or cellular component: Lamellar body in A549 cells expressing ABCA3-eGFP

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Supramolecule #1: Lamellar body in A549 cells expressing ABCA3-eGFP

SupramoleculeName: Lamellar body in A549 cells expressing ABCA3-eGFP / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.3 nA / Focused ion beam - Duration: 1 sec. / Focused ion beam - Temperature: 100 K / Focused ion beam - Initial thickness: 10000 nm / Focused ion beam - Final thickness: 200 nm
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

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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 K3 BIOQUANTUM (6k x 4k) / 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 reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 41

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