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Yorodumi- EMDB-23622: Cryo-electron tomogram of FIB-milled Caulobacter crescentus expre... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23622 | ||||||||||||
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Title | Cryo-electron tomogram of FIB-milled Caulobacter crescentus expressing WT PopZ | ||||||||||||
Map data | Caulobacter crescentus cells expressing wildtype PopZ | ||||||||||||
Sample |
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Biological species | Caulobacter vibrioides NA1000 (bacteria) | ||||||||||||
Method | electron tomography / cryo EM | ||||||||||||
Authors | Lasker K / Boeynaems S / Lam V / Scholl D / Stainton E / Briner A / Jacquemyn M / Daelemans D / Deniz A / Villa E ...Lasker K / Boeynaems S / Lam V / Scholl D / Stainton E / Briner A / Jacquemyn M / Daelemans D / Deniz A / Villa E / Holehouse AS / Gitler AD / Shapiro L | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Nat Commun / Year: 2022 Title: The material properties of a bacterial-derived biomolecular condensate tune biological function in natural and synthetic systems Authors: Lasker K / Boeynaems S / Lam V / Scholl D / Stainton E / Briner A / Jacquemyn M / Daelemans D / Deniz A / Villa E / Holehouse AS / Gitler AD / Shapiro L #1: Journal: biorxiv / Year: 2021 Title: A modular platform for engineering function of natural and synthetic biomolecular condensates Authors: Lasker K / Boeynaems S / Lam V / Stainton E / Jacquemyn M / Daelemans D / Villa E / Holehouse AS / Gitler AD / Shapiro L | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_23622.map.gz | 93.7 MB | EMDB map data format | |
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Header (meta data) | emd-23622-v30.xml emd-23622.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
Images | emd_23622.png | 271.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23622 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23622 | HTTPS FTP |
-Validation report
Summary document | emd_23622_validation.pdf.gz | 445.9 KB | Display | EMDB validaton report |
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Full document | emd_23622_full_validation.pdf.gz | 445.5 KB | Display | |
Data in XML | emd_23622_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | emd_23622_validation.cif.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23622 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23622 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_23622.map.gz / Format: CCP4 / Size: 152.9 MB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||
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Annotation | Caulobacter crescentus cells expressing wildtype PopZ | ||||||||||||||||||||
Voxel size | X=Y=Z: 17.32 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Caulobacter crescentus cells expressing WT PopZ
Entire | Name: Caulobacter crescentus cells expressing WT PopZ |
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Components |
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-Supramolecule #1: Caulobacter crescentus cells expressing WT PopZ
Supramolecule | Name: Caulobacter crescentus cells expressing WT PopZ / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Caulobacter vibrioides NA1000 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 / Details: M2 minimal media, supplemented with glucose. |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.019 kPa / Details: 20 mA current. Instrumet: PELCO easiGlow |
Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER |
Details | Protein expression was induced 4-5 hours prior to plunge freezing. Cells were concentrated to an OD600 ~3.0 by centrifugation. |
Cryo protectant | Trehalose |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.01 nA / Focused ion beam - Duration: 2700 sec. / Focused ion beam - Temperature: 77 K / Focused ion beam - Initial thickness: 500 nm / Focused ion beam - Final thickness: 150 nm Focused ion beam - Details: milling current varies from 0.5 nA to 10 pA during milling.. The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Aquilos Cryo-FIB. This is not in a list ...Focused ion beam - Details: milling current varies from 0.5 nA to 10 pA during milling.. The value given for _emd_sectioning_focused_ion_beam.instrument is FEI Aquilos Cryo-FIB. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 77.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3708 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-15 / Number real images: 61 / Average exposure time: 1.45 sec. / Average electron dose: 2.16 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus min: 5.0 µm / Nominal magnification: 33000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.10.29) / Number images used: 61 |
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