[English] 日本語
Yorodumi- EMDB-23624: Caulobacter crescentus expressing PopZ with IDR-156 and pentavalent OD -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23624 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Caulobacter crescentus expressing PopZ with IDR-156 and pentavalent OD | ||||||||||||
Map data | Caulobacter crescentus expressing mCherry-PopZ with IDR-156 and pentavalent OD. | ||||||||||||
Sample |
| ||||||||||||
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
| ||||||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_23624.map.gz | 60.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-23624-v30.xml emd-23624.xml | 13.9 KB 13.9 KB | Display Display | EMDB header |
Images | emd_23624.png | 268.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23624 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23624 | HTTPS FTP |
-Validation report
Summary document | emd_23624_validation.pdf.gz | 423.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_23624_full_validation.pdf.gz | 423 KB | Display | |
Data in XML | emd_23624_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | emd_23624_validation.cif.gz | 4.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23624 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23624 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_23624.map.gz / Format: CCP4 / Size: 85.8 MB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Caulobacter crescentus expressing mCherry-PopZ with IDR-156 and pentavalent OD. | ||||||||||||||||||||
Voxel size | X=Y=Z: 17.06 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Sample components
-Entire : Caulobacter crescentus cells expressing PopZ with IDR-156 and pen...
Entire | Name: Caulobacter crescentus cells expressing PopZ with IDR-156 and pentavalent OD. |
---|---|
Components |
|
-Supramolecule #1: Caulobacter crescentus cells expressing PopZ with IDR-156 and pen...
Supramolecule | Name: Caulobacter crescentus cells expressing PopZ with IDR-156 and pentavalent OD. type: cell / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Caulobacter vibrioides NA1000 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 / Details: M2 minimal media, supplemented with glucose. |
---|---|
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: current: 20 mA Instrument: 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 |
---|---|
Temperature | Min: 77.0 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 30 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-15 / Number real images: 51 / Average exposure time: 1.41 sec. / Average electron dose: 1.93 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: 51 |
---|