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- EMDB-29788: Structure of WT E.coli ribosome 50S subunit with complexed with m... -
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Open data
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Basic information
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Title | Structure of WT E.coli ribosome 50S subunit with complexed with mRNA, P-site fMet-NH-tRNAfMet and A-site 3-aminopyridine-4-carboxylic acid charged NH-tRNAPhe | |||||||||
![]() | 50S focus refined map | |||||||||
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![]() | ribosome / non-natural monomers / aminobenzoic acids / unnatural monomers | |||||||||
Function / homology | ![]() negative regulation of cytoplasmic translational initiation / positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / translational initiation / regulation of cell growth ...negative regulation of cytoplasmic translational initiation / positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / translational initiation / regulation of cell growth / large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.09 Å | |||||||||
![]() | Majumdar C / Cate JHD | |||||||||
Funding support | ![]()
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![]() | ![]() 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. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 55.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 51.4 KB 51.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.4 KB | Display | ![]() |
Images | ![]() | 82.8 KB | ||
Filedesc metadata | ![]() | 11.3 KB | ||
Others | ![]() ![]() | 373.1 MB 373.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8g6yMC ![]() 8g6wC ![]() 8g6xC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | 50S focus refined map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.824 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: 50S focus refinement half map
File | emd_29788_half_map_1.map | ||||||||||||
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Annotation | 50S focus refinement half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: 50S focus refinement half map
File | emd_29788_half_map_2.map | ||||||||||||
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Annotation | 50S focus refinement half map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : 50S subunit of E.coli ribosome
+Supramolecule #1: 50S subunit of E.coli ribosome
+Macromolecule #1: 50S ribosomal protein L33
+Macromolecule #2: 50S ribosomal protein L34
+Macromolecule #3: 50S ribosomal protein L35
+Macromolecule #4: 50S ribosomal protein L36
+Macromolecule #5: 50S ribosomal protein L31
+Macromolecule #11: 50S ribosomal protein L2
+Macromolecule #12: 50S ribosomal protein L3
+Macromolecule #13: 50S ribosomal protein L4
+Macromolecule #14: 50S ribosomal protein L5
+Macromolecule #15: 50S ribosomal protein L6
+Macromolecule #16: 50S ribosomal protein L9
+Macromolecule #17: 50S ribosomal protein L13
+Macromolecule #18: 50S ribosomal protein L14
+Macromolecule #19: 50S ribosomal protein L15
+Macromolecule #20: 50S ribosomal protein L16
+Macromolecule #21: 50S ribosomal protein L17
+Macromolecule #22: 50S ribosomal protein L18
+Macromolecule #23: 50S ribosomal protein L19
+Macromolecule #24: 50S ribosomal protein L20
+Macromolecule #25: Ribosomal protein L21
+Macromolecule #26: 50S ribosomal protein L22
+Macromolecule #27: 50S ribosomal protein L23
+Macromolecule #28: 50S ribosomal protein L24
+Macromolecule #29: 50S ribosomal protein L25
+Macromolecule #30: 50S ribosomal protein L27
+Macromolecule #31: 50S ribosomal protein L28
+Macromolecule #32: 50S ribosomal protein L29
+Macromolecule #33: 50S ribosomal protein L30
+Macromolecule #34: 50S ribosomal protein L32
+Macromolecule #6: mRNA
+Macromolecule #7: A-site tRNA Phe
+Macromolecule #8: P-site tRNA fMet
+Macromolecule #9: 23S rRNA
+Macromolecule #10: 5S rRNA
+Macromolecule #35: ZINC ION
+Macromolecule #36: 3-aminopyridine-4-carboxamide
+Macromolecule #37: 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate)
+Macromolecule #38: N-FORMYLMETHIONINE
+Macromolecule #39: MAGNESIUM ION
+Macromolecule #40: POTASSIUM ION
+Macromolecule #41: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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: ![]() |
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 |