+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10444 | |||||||||
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Title | Sub-tomogram average of the Sulfolobus acidocaldarius S-layer | |||||||||
Map data | Sub-tomogram average of the Sulfolobus acidocaldarius S-layer | |||||||||
Sample |
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Biological species | Sulfolobus acidocaldarius (acidophilic) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 23.0 Å | |||||||||
Authors | Daum B / Gambelli L | |||||||||
Funding support | United Kingdom, 1 items
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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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10444.map.gz | 5.3 MB | EMDB map data format | |
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Header (meta data) | emd-10444-v30.xml emd-10444.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | emd_10444.png | 55.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10444 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10444 | HTTPS FTP |
-Validation report
Summary document | emd_10444_validation.pdf.gz | 245.2 KB | Display | EMDB validaton report |
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Full document | emd_10444_full_validation.pdf.gz | 244.4 KB | Display | |
Data in XML | emd_10444_validation.xml.gz | 4.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10444 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10444 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10444.map.gz / Format: CCP4 / Size: 5.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sub-tomogram average of the Sulfolobus acidocaldarius S-layer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 7.70655 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : SlaA/SlaB array
Entire | Name: SlaA/SlaB array |
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Components |
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-Supramolecule #1: SlaA/SlaB array
Supramolecule | Name: SlaA/SlaB array / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Sulfolobus acidocaldarius (acidophilic) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | 2D array |
-Sample preparation
Buffer | pH: 3 |
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Grid | Model: Quantifoil R2/2 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Specialist optics | Energy filter - Slit width: 40 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.33 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |
-Image processing
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Software - Name: PEET / Number subtomograms used: 325 |
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Extraction | Number tomograms: 1 / Number images used: 325 |
CTF correction | Software - Name: IMOD |
Final angle assignment | Type: OTHER / Software - Name: PEET |