+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23661 | |||||||||||||||
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Title | Cryo-electron tomogram of a JCVI_Syn3A cell | |||||||||||||||
Map data | cryo-electron tomogram of a JCVI_Syn3A cell | |||||||||||||||
Sample |
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Biological species | synthetic bacterium JCVI-Syn3A (others) | |||||||||||||||
Method | electron tomography / cryo EM | |||||||||||||||
Authors | Lam V / Villa E | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Front Mol Biosci / Year: 2021 Title: Generating Chromosome Geometries in a Minimal Cell From Cryo-Electron Tomograms and Chromosome Conformation Capture Maps. Authors: Benjamin R Gilbert / Zane R Thornburg / Vinson Lam / Fatema-Zahra M Rashid / John I Glass / Elizabeth Villa / Remus T Dame / Zaida Luthey-Schulten / Abstract: JCVI-syn3A is a genetically minimal bacterial cell, consisting of 493 genes and only a single 543 kbp circular chromosome. Syn3A's genome and physical size are approximately one-tenth those of the ...JCVI-syn3A is a genetically minimal bacterial cell, consisting of 493 genes and only a single 543 kbp circular chromosome. Syn3A's genome and physical size are approximately one-tenth those of the model bacterial organism 's, and the corresponding reduction in complexity and scale provides a unique opportunity for whole-cell modeling. Previous work established genome-scale gene essentiality and proteomics data along with its essential metabolic network and a kinetic model of genetic information processing. In addition to that information, whole-cell, spatially-resolved kinetic models require cellular architecture, including spatial distributions of ribosomes and the circular chromosome's configuration. We reconstruct cellular architectures of Syn3A cells at the single-cell level directly from cryo-electron tomograms, including the ribosome distributions. We present a method of generating self-avoiding circular chromosome configurations in a lattice model with a resolution of 11.8 bp per monomer on a 4 nm cubic lattice. Realizations of the chromosome configurations are constrained by the ribosomes and geometry reconstructed from the tomograms and include DNA loops suggested by experimental chromosome conformation capture (3C) maps. Using ensembles of simulated chromosome configurations we predict chromosome contact maps for Syn3A cells at resolutions of 250 bp and greater and compare them to the experimental maps. Additionally, the spatial distributions of ribosomes and the DNA-crowding resulting from the individual chromosome configurations can be used to identify macromolecular structures formed from ribosomes and DNA, such as polysomes and expressomes. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23661.map.gz | 48.5 MB | EMDB map data format | |
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Header (meta data) | emd-23661-v30.xml emd-23661.xml | 10.4 KB 10.4 KB | Display Display | EMDB header |
Images | emd_23661.png | 139.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23661 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23661 | HTTPS FTP |
-Validation report
Summary document | emd_23661_validation.pdf.gz | 253.2 KB | Display | EMDB validaton report |
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Full document | emd_23661_full_validation.pdf.gz | 252.8 KB | Display | |
Data in XML | emd_23661_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | emd_23661_validation.cif.gz | 5.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23661 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23661 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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EM raw data | EMPIAR-10686 (Title: Cryo-electron tomography of JCVI-Syn3A (small cell) / Data size: 6.4 Data #1: Unaligned Tilt-series of JCVI-Syn3A (small cell) [tilt series] Data #2: Multi-frame micrographs of each tilt for tilt-series of JCVI-Syn3A (small cell) [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_23661.map.gz / Format: CCP4 / Size: 77.3 MB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | cryo-electron tomogram of a JCVI_Syn3A cell | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 17.06 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 : Cryo-electron tomogram of whole JCVI-Syn3A synthetic mycoplasma.
Entire | Name: Cryo-electron tomogram of whole JCVI-Syn3A synthetic mycoplasma. |
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Components |
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-Supramolecule #1: Cryo-electron tomogram of whole JCVI-Syn3A synthetic mycoplasma.
Supramolecule | Name: Cryo-electron tomogram of whole JCVI-Syn3A synthetic mycoplasma. type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: synthetic bacterium JCVI-Syn3A (others) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 / Details: nominal pH of SP4 medium |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / 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 | grown in SP4 medium to mid-log phase |
Sectioning | Other: NO SECTIONING |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 77.0 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 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: 1-8 / Average exposure time: 1.98 sec. / Average electron dose: 1.72 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: 6.0 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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