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Yorodumi- EMDB-28256: 30S-focused map for: "Atomistic simulations of the E. coli riboso... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28256 | |||||||||
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Title | 30S-focused map for: "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates" | |||||||||
Map data | Post-processed, masked 30S-focused map | |||||||||
Sample |
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Keywords | ribosome / tRNA / e. coli | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
Authors | Watson ZL / Cate JHD | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Chem / Year: 2023 Title: Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates. Authors: Zoe L Watson / Isaac J Knudson / Fred R Ward / Scott J Miller / Jamie H D Cate / Alanna Schepartz / Ara M Abramyan / Abstract: As genetic code expansion advances beyond L-α-amino acids to backbone modifications and new polymerization chemistries, delineating what substrates the ribosome can accommodate remains a challenge. ...As genetic code expansion advances beyond L-α-amino acids to backbone modifications and new polymerization chemistries, delineating what substrates the ribosome can accommodate remains a challenge. The Escherichia coli ribosome tolerates non-L-α-amino acids in vitro, but few structural insights that explain how are available, and the boundary conditions for efficient bond formation are so far unknown. Here we determine a high-resolution cryogenic electron microscopy structure of the E. coli ribosome containing α-amino acid monomers and use metadynamics simulations to define energy surface minima and understand incorporation efficiencies. Reactive monomers across diverse structural classes favour a conformational space where the aminoacyl-tRNA nucleophile is <4 Å from the peptidyl-tRNA carbonyl with a Bürgi-Dunitz angle of 76-115°. Monomers with free energy minima that fall outside this conformational space do not react efficiently. This insight should accelerate the in vivo and in vitro ribosomal synthesis of sequence-defined, non-peptide heterooligomers. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28256.map.gz | 30.6 MB | EMDB map data format | |
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Header (meta data) | emd-28256-v30.xml emd-28256.xml | 22.3 KB 22.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28256_fsc.xml | 16.1 KB | Display | FSC data file |
Images | emd_28256.png | 104.4 KB | ||
Masks | emd_28256_msk_1.map | 361.7 MB | Mask map | |
Others | emd_28256_additional_1.map.gz emd_28256_half_map_1.map.gz emd_28256_half_map_2.map.gz | 288.4 MB 289.6 MB 289.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28256 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28256 | HTTPS FTP |
-Validation report
Summary document | emd_28256_validation.pdf.gz | 899.1 KB | Display | EMDB validaton report |
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Full document | emd_28256_full_validation.pdf.gz | 898.6 KB | Display | |
Data in XML | emd_28256_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | emd_28256_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28256 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28256 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_28256.map.gz / Format: CCP4 / Size: 361.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Post-processed, masked 30S-focused map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8296 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_28256_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Map from 30S-focused 3D auto-refine, without post-processing
File | emd_28256_additional_1.map | ||||||||||||
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Annotation | Map from 30S-focused 3D auto-refine, without post-processing | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half-map 1
File | emd_28256_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half-map 2
File | emd_28256_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 30S-focused map
Entire | Name: 30S-focused map |
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Components |
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-Supramolecule #1: 30S-focused map
Supramolecule | Name: 30S-focused map / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#54 Details: Overall complex includes 70S ribosome with mRNA, A- and P-site Met-NH-tRNAs |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |