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Yorodumi- EMDB-29790: 30S focus refined map of WT E.coli ribosome complexed with A-site... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29790 | |||||||||
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Title | 30S focus refined map of WT E.coli ribosome complexed with A-site ortho-aminobenzoic acid charged tRNA-Phe | |||||||||
Map data | 30S focus refined map | |||||||||
Sample |
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Keywords | ribosome / non-natural monomers / aminobenzoic acids / unnatural monomers | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.14 Å | |||||||||
Authors | Majumdar C / Cate JHD | |||||||||
Funding support | United States, 1 items
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Citation | Journal: ACS Cent Sci / Year: 2023 Title: Aminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome. Authors: Chandrima Majumdar / Joshua A Walker / Matthew B Francis / Alanna Schepartz / Jamie H D Cate / Abstract: The () ribosome can incorporate a variety of non-l-α-amino acid monomers into polypeptide chains but with poor efficiency. Although these monomers span a diverse set of compounds, there exists no ...The () ribosome can incorporate a variety of non-l-α-amino acid monomers into polypeptide chains but with poor efficiency. Although these monomers span a diverse set of compounds, there exists no high-resolution structural information regarding their positioning within the catalytic center of the ribosome, the peptidyl transferase center (PTC). Thus, details regarding the mechanism of amide bond formation and the structural basis for differences and defects in incorporation efficiency remain unknown. Within a set of three aminobenzoic acid derivatives-3-aminopyridine-4-carboxylic acid (Apy), aminobenzoic acid (ABZ), and aminobenzoic acid (ABZ)-the ribosome incorporates Apy into polypeptide chains with the highest efficiency, followed by ABZ and then ABZ, a trend that does not track with the nucleophilicity of the reactive amines. Here, we report high-resolution cryo-EM structures of the ribosome with each of these three aminobenzoic acid derivatives charged on tRNA bound in the aminoacyl-tRNA site (A-site). The structures reveal how the aromatic ring of each monomer sterically blocks the positioning of nucleotide U2506, thereby preventing rearrangement of nucleotide U2585 and the resulting induced fit in the PTC required for efficient amide bond formation. They also reveal disruptions to the bound water network that is believed to facilitate formation and breakdown of the tetrahedral intermediate. Together, the cryo-EM structures reported here provide a mechanistic rationale for differences in reactivity of aminobenzoic acid derivatives relative to l-α-amino acids and each other and identify stereochemical constraints on the size and geometry of non-monomers that can be accepted efficiently by wild-type ribosomes. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29790.map.gz | 46.7 MB | EMDB map data format | |
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Header (meta data) | emd-29790-v30.xml emd-29790.xml | 20.1 KB 20.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29790_fsc.xml | 16.3 KB | Display | FSC data file |
Images | emd_29790.png | 89.1 KB | ||
Filedesc metadata | emd-29790.cif.gz | 4.1 KB | ||
Others | emd_29790_half_map_1.map.gz emd_29790_half_map_2.map.gz | 304.6 MB 304.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29790 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29790 | HTTPS FTP |
-Validation report
Summary document | emd_29790_validation.pdf.gz | 888.4 KB | Display | EMDB validaton report |
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Full document | emd_29790_full_validation.pdf.gz | 887.9 KB | Display | |
Data in XML | emd_29790_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | emd_29790_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29790 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29790 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_29790.map.gz / Format: CCP4 / Size: 381.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | 30S focus refined map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8232 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: 30S focus refinement half map
File | emd_29790_half_map_1.map | ||||||||||||
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Annotation | 30S focus refinement half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: 30S focus refinement half map
File | emd_29790_half_map_2.map | ||||||||||||
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Annotation | 30S focus refinement half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 70S E.coli ribosome
Entire | Name: 70S E.coli ribosome |
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Components |
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-Supramolecule #1: 70S E.coli ribosome
Supramolecule | Name: 70S E.coli ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#55 |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: MRE600 |
-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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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (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: 1.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |