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- EMDB-10460: Sub-tomogram average of the Sulfolobus acidocaldarius S-layer in situ -

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Basic information

Entry
Database: EMDB / ID: EMD-10460
TitleSub-tomogram average of the Sulfolobus acidocaldarius S-layer in situ
Map dataSub-tomogram averaging of the Sulfolobus acidocaldarius S-layer.
Sample
  • Complex: SlaA/SlaB array
Biological speciesSulfolobus islandicus (acidophilic)
Methodsubtomogram averaging / cryo EM / Resolution: 56.0 Å
AuthorsDaum B / Gambelli L
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
European Research Council803894 United Kingdom
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2019
Title: Architecture and modular assembly of S-layers revealed by electron cryotomography.
Authors: Lavinia Gambelli / Benjamin H Meyer / Mathew McLaren / Kelly Sanders / Tessa E F Quax / Vicki A M Gold / Sonja-Verena Albers / Bertram Daum /
Abstract: Surface protein layers (S-layers) often form the only structural component of the archaeal cell wall and are therefore important for cell survival. S-layers have a plethora of cellular functions ...Surface protein layers (S-layers) often form the only structural component of the archaeal cell wall and are therefore important for cell survival. S-layers have a plethora of cellular functions including maintenance of cell shape, osmotic, and mechanical stability, the formation of a semipermeable protective barrier around the cell, and cell-cell interaction, as well as surface adhesion. Despite the central importance of S-layers for archaeal life, their 3-dimensional (3D) architecture is still poorly understood. Here we present detailed 3D electron cryomicroscopy maps of archaeal S-layers from 3 different strains. We were able to pinpoint the positions and determine the structure of the 2 subunits SlaA and SlaB. We also present a model describing the assembly of the mature S-layer.
#1: Journal: To Be Published
Title: Architecture and modular assembly of Sulfolobus S-layers revealed by electron cryo-tomography
Authors: Gambelli L / Meyer BH / McLaren M / Sanders K / Quax TEF / Gold VAM / Albers SVA / Daum B
History
DepositionNov 6, 2019-
Header (metadata) releaseNov 27, 2019-
Map releaseNov 27, 2019-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 169.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 169.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10460.png

Downloads & links

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Map

FileDownload / File: emd_10460.map.gz / Format: CCP4 / Size: 1.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSub-tomogram averaging of the Sulfolobus acidocaldarius S-layer.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.73 Å/pix.
x 60 pix.
= 643.8 Å		10.73 Å/pix.
x 80 pix.
= 858.4 Å		10.73 Å/pix.
x 80 pix.
= 858.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 10.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 169.5 / Movie #1: 169.5
Minimum - Maximum164.04999 - 174.12
Average (Standard dev.)168.78543 (±0.5882491)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-203
Dimensions808060
Spacing808060
CellA: 858.39996 Å / B: 858.39996 Å / C: 643.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z10.7310.7310.73
M x/y/z808060
origin x/y/z0.0000.0000.000
length x/y/z858.400858.400643.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS0-23
NC/NR/NS808060
D min/max/mean164.050174.120168.785

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Supplemental data

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Sample components

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Entire : SlaA/SlaB array

EntireName: SlaA/SlaB array
Components
  • Complex: SlaA/SlaB array

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Supramolecule #1: SlaA/SlaB array

SupramoleculeName: SlaA/SlaB array / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Sulfolobus islandicus (acidophilic)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state2D array

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Sample preparation

BufferpH: 3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Specialist opticsEnergy filter - Slit width: 40 eV
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / #0 - Detector mode: COUNTING / #0 - Average electron dose: 1.8 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / #1 - Average electron dose: 1.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Image recording ID1
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 56.0 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Software - Name: PEET / Number subtomograms used: 2068
ExtractionNumber tomograms: 1 / Number images used: 2068
CTF correctionSoftware - Name: IMOD
Final angle assignmentType: OTHER / Software - Name: PEET

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