[English] 日本語
Yorodumi- EMDB-28165: E. coli 70S ribosome with A-loop mutations U2554C and U2555C (Com... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28165 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | E. coli 70S ribosome with A-loop mutations U2554C and U2555C (Composite Map) | |||||||||
Map data | 70S E. coli Ribosome with U2554C U2555C A-loop Mutations (Composite Map) | |||||||||
Sample |
| |||||||||
Keywords | RNA / thermophile / A loop / RIBOSOME | |||||||||
Function / homology | Function and homology information negative regulation of cytoplasmic translational initiation / positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly ...negative regulation of cytoplasmic translational initiation / positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / transcription antitermination / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.24 Å | |||||||||
Authors | Nissley AJ / Penev PI / Watson ZL / Banfield JF / Cate JHD | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: Nucleic Acids Res / Year: 2023 Title: Rare ribosomal RNA sequences from archaea stabilize the bacterial ribosome. Authors: Amos J Nissley / Petar I Penev / Zoe L Watson / Jillian F Banfield / Jamie H D Cate / Abstract: The ribosome serves as the universally conserved translator of the genetic code into proteins and supports life across diverse temperatures ranging from below freezing to above 120°C. Ribosomes are ...The ribosome serves as the universally conserved translator of the genetic code into proteins and supports life across diverse temperatures ranging from below freezing to above 120°C. Ribosomes are capable of functioning across this wide range of temperatures even though the catalytic site for peptide bond formation, the peptidyl transferase center, is nearly universally conserved. Here we find that Thermoproteota, a phylum of thermophilic Archaea, substitute cytidine for uridine at large subunit rRNA positions 2554 and 2555 (Escherichia coli numbering) in the A loop, immediately adjacent to the binding site for the 3'-end of A-site tRNA. We show by cryo-EM that E. coli ribosomes with uridine to cytidine mutations at these positions retain the proper fold and post-transcriptional modification of the A loop. Additionally, these mutations do not affect cellular growth, protect the large ribosomal subunit from thermal denaturation, and increase the mutational robustness of nucleotides in the peptidyl transferase center. This work identifies sequence variation across archaeal ribosomes in the peptidyl transferase center that likely confers stabilization of the ribosome at high temperatures and develops a stable mutant bacterial ribosome that can act as a scaffold for future ribosome engineering efforts. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_28165.map.gz | 30.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-28165-v30.xml emd-28165.xml | 85 KB 85 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28165_fsc.xml | 15.5 KB | Display | FSC data file |
Images | emd_28165.png | 155.1 KB | ||
Filedesc metadata | emd-28165.cif.gz | 15.2 KB | ||
Others | emd_28165_additional_1.map.gz emd_28165_half_map_1.map.gz emd_28165_half_map_2.map.gz | 304.3 MB 260.2 MB 260.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28165 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28165 | HTTPS FTP |
-Validation report
Summary document | emd_28165_validation.pdf.gz | 963.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_28165_full_validation.pdf.gz | 963.1 KB | Display | |
Data in XML | emd_28165_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | emd_28165_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28165 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28165 | HTTPS FTP |
-Related structure data
Related structure data | 8eiuMC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_28165.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | 70S E. coli Ribosome with U2554C U2555C A-loop Mutations (Composite Map) | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8279 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: 70S E. coli Ribosome with U2554C U2555C A-loop Mutations (Global Map)
File | emd_28165_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | 70S E. coli Ribosome with U2554C U2555C A-loop Mutations (Global Map) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: 70S E. coli Ribosome with U2554C U2555C A-loop...
File | emd_28165_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | 70S E. coli Ribosome with U2554C U2555C A-loop Mutations (Global Half Map) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: 70S E. coli Ribosome with U2554C U2555C A-loop...
File | emd_28165_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | 70S E. coli Ribosome with U2554C U2555C A-loop Mutations (Global Half Map) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : E. coli 70S ribosome with A-loop mutations U2554C and U2555C
+Supramolecule #1: E. coli 70S ribosome with A-loop mutations U2554C and U2555C
+Supramolecule #2: 50S Subunit
+Supramolecule #3: 30S Subunit
+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 #7: 30S ribosomal protein S2
+Macromolecule #8: 30S ribosomal protein S3
+Macromolecule #9: 30S ribosomal protein S4
+Macromolecule #10: 30S ribosomal protein S5
+Macromolecule #11: 30S ribosomal protein S6
+Macromolecule #12: 30S ribosomal protein S7
+Macromolecule #13: 30S ribosomal protein S8
+Macromolecule #14: 30S ribosomal protein S9
+Macromolecule #15: 30S ribosomal protein S10
+Macromolecule #16: 30S ribosomal protein S11
+Macromolecule #17: 30S ribosomal protein S12
+Macromolecule #18: 30S ribosomal protein S13
+Macromolecule #19: 30S ribosomal protein S14
+Macromolecule #20: 30S ribosomal protein S15
+Macromolecule #21: 30S ribosomal protein S16
+Macromolecule #22: 30S ribosomal protein S17
+Macromolecule #23: 30S ribosomal protein S18
+Macromolecule #24: 30S ribosomal protein S19
+Macromolecule #25: 30S ribosomal protein S20
+Macromolecule #26: 30S ribosomal protein S21
+Macromolecule #31: 50S ribosomal protein L2
+Macromolecule #32: 50S ribosomal protein L3
+Macromolecule #33: 50S ribosomal protein L4
+Macromolecule #34: 50S ribosomal protein L5
+Macromolecule #35: 50S ribosomal protein L6
+Macromolecule #36: 50S ribosomal protein L9
+Macromolecule #37: 50S ribosomal protein L13
+Macromolecule #38: 50S ribosomal protein L14
+Macromolecule #39: 50S ribosomal protein L15
+Macromolecule #40: 50S ribosomal protein L16
+Macromolecule #41: 50S ribosomal protein L17
+Macromolecule #42: 50S ribosomal protein L18
+Macromolecule #43: 50S ribosomal protein L19
+Macromolecule #44: 50S ribosomal protein L20
+Macromolecule #45: Ribosomal protein L21
+Macromolecule #46: 50S ribosomal protein L22
+Macromolecule #47: 50S ribosomal protein L23
+Macromolecule #48: 50S ribosomal protein L24
+Macromolecule #49: 50S ribosomal protein L25
+Macromolecule #50: 50S ribosomal protein L27
+Macromolecule #51: 50S ribosomal protein L28
+Macromolecule #52: 50S ribosomal protein L29
+Macromolecule #53: 50S ribosomal protein L30
+Macromolecule #54: 50S ribosomal protein L32
+Macromolecule #6: 16S rRNA
+Macromolecule #27: mRNA
+Macromolecule #28: tRNA-fMET
+Macromolecule #29: 23S rRNA
+Macromolecule #30: 5S rRNA
+Macromolecule #55: ZINC ION
+Macromolecule #56: PAROMOMYCIN
+Macromolecule #57: MAGNESIUM ION
+Macromolecule #58: SPERMIDINE
+Macromolecule #59: 3'-amino-3'-deoxyadenosine 5'-(dihydrogen phosphate)
+Macromolecule #60: SPERMINE
+Macromolecule #61: METHIONINE
+Macromolecule #62: water
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.5 Component:
| ||||||||||||||||
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 12 sec. | ||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / 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 / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |