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- EMDB-49594: Cryo-EM structure of the wild-type Thermus thermophilus 70S ribos... -
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Open data
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Basic information
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Title | Cryo-EM structure of the wild-type Thermus thermophilus 70S ribosome in complex with mRNA, A-site Q230-N5-methylated Release Factor 1, and P-site 2'-deoxy-A76-fMEAAAKC-peptidyl-tRNAcys at 2.13A resolution | |||||||||||||||||||||
![]() | Full map of Thermus thermophilus 70S ribosome with 2'deoxy-A76-peptidyl-tRNA and release factor 1 | |||||||||||||||||||||
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![]() | Translation termination / peptide release / release factor / hydrolysis / peptidyl-tRNA / 70S ribosome / cryo-EM / pre-termination state / peptidyl transferase center / RIBOSOME | |||||||||||||||||||||
Function / homology | ![]() translation release factor activity, codon specific / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding ...translation release factor activity, codon specific / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.13 Å | |||||||||||||||||||||
![]() | Aleksandrova EV / Syroegin EA / Basu RS / Vassilevski AA / Gagnon MG / Polikanov YS | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of release factor-mediated peptidyl-tRNA hydrolysis on the ribosome. Authors: Elena V Aleksandrova / Egor A Syroegin / Ritwika S Basu / Alexander A Vassilevski / Matthieu G Gagnon / Yury S Polikanov / ![]() ![]() Abstract: Translation termination is essential in all living organisms because it ensures that proteins have lengths strictly defined by their genes. This universal process is mediated by peptide release ...Translation termination is essential in all living organisms because it ensures that proteins have lengths strictly defined by their genes. This universal process is mediated by peptide release factors (RFs) that recognize stop codons and catalyze the hydrolysis of peptidyl transfer RNA (peptidyl-tRNA) on the ribosome, presumably by activating a water molecule. We report structures of the bacterial ribosome in complex with peptidyl-tRNA and RFs in the prepeptide release state. No hydrolytic water molecule was seen in the peptidyl transferase center. Instead, RFs induced rearrangements of the peptidyl-tRNA adenine 76 (A76) ribose pucker that orient the 2'-OH for the nucleophilic attack onto the neighboring carbonyl group. These findings suggest a catalytic mechanism of RF-mediated peptide release and provide a structural basis for the universal conservation of the catalytic domain in peptide RFs. | |||||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 258.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 82 KB 82 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.8 KB | Display | ![]() |
Images | ![]() | 236.7 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Filedesc metadata | ![]() | 15.7 KB | ||
Others | ![]() ![]() ![]() | 484.2 MB 474.7 MB 474.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 26.4 KB | Display | |
Data in CIF | ![]() | 34.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9no7MC ![]() 9mtpC ![]() 9mtqC ![]() 9mtrC ![]() 9mtsC ![]() 9mttC 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 | Full map of Thermus thermophilus 70S ribosome with 2'deoxy-A76-peptidyl-tRNA and release factor 1 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8423 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: Sharpened map of Thermus thermophilus 70S ribosome with...
File | emd_49594_additional_1.map | ||||||||||||
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Annotation | Sharpened map of Thermus thermophilus 70S ribosome with 2'deoxy-A76-peptidyl-tRNA and release factor 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of Thermus thermophilus 70S ribosome with...
File | emd_49594_half_map_1.map | ||||||||||||
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Annotation | Half map of Thermus thermophilus 70S ribosome with 2'deoxy-A76-peptidyl-tRNA and release factor 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of Thermus thermophilus 70S ribosome with...
File | emd_49594_half_map_2.map | ||||||||||||
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Annotation | Half map of Thermus thermophilus 70S ribosome with 2'deoxy-A76-peptidyl-tRNA and release factor 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Thermus thermophilus 70S ribosome in complex with mRNA, A-site Q2...
+Supramolecule #1: Thermus thermophilus 70S ribosome in complex with mRNA, A-site Q2...
+Macromolecule #1: 23S Ribosomal RNA
+Macromolecule #2: 5S Ribosomal RNA
+Macromolecule #32: 16S Ribosomal RNA
+Macromolecule #53: CYS-Stop mRNA
+Macromolecule #55: P-site Peptidyl-tRNA fMEAAAKC-tRNAcys RNA-part
+Macromolecule #3: 50S ribosomal protein L2
+Macromolecule #4: 50S ribosomal protein L3
+Macromolecule #5: 50S ribosomal protein L4
+Macromolecule #6: 50S ribosomal protein L5
+Macromolecule #7: 50S ribosomal protein L6
+Macromolecule #8: 50S ribosomal protein L9
+Macromolecule #9: 50S ribosomal protein L13
+Macromolecule #10: 50S ribosomal protein L14
+Macromolecule #11: 50S ribosomal protein L15
+Macromolecule #12: 50S ribosomal protein L16
+Macromolecule #13: 50S ribosomal protein L17
+Macromolecule #14: 50S ribosomal protein L18
+Macromolecule #15: 50S ribosomal protein L19
+Macromolecule #16: 50S ribosomal protein L20
+Macromolecule #17: 50S ribosomal protein L21
+Macromolecule #18: 50S ribosomal protein L22
+Macromolecule #19: 50S ribosomal protein L23
+Macromolecule #20: 50S ribosomal protein L24
+Macromolecule #21: 50S ribosomal protein L25
+Macromolecule #22: 50S ribosomal protein L27
+Macromolecule #23: 50S ribosomal protein L28
+Macromolecule #24: 50S ribosomal protein L29
+Macromolecule #25: 50S ribosomal protein L30
+Macromolecule #26: 50S ribosomal protein L31
+Macromolecule #27: 50S ribosomal protein L32
+Macromolecule #28: 50S ribosomal protein L33
+Macromolecule #29: 50S ribosomal protein L34
+Macromolecule #30: 50S ribosomal protein L35
+Macromolecule #31: 50S ribosomal protein L36
+Macromolecule #33: 30S ribosomal protein S2
+Macromolecule #34: 30S ribosomal protein S3
+Macromolecule #35: 30S ribosomal protein S4
+Macromolecule #36: 30S ribosomal protein S5
+Macromolecule #37: 30S ribosomal protein S6
+Macromolecule #38: 30S ribosomal protein S7
+Macromolecule #39: 30S ribosomal protein S8
+Macromolecule #40: 30S ribosomal protein S9
+Macromolecule #41: 30S ribosomal protein S10
+Macromolecule #42: 30S ribosomal protein S11
+Macromolecule #43: 30S ribosomal protein S12
+Macromolecule #44: 30S ribosomal protein S13
+Macromolecule #45: 30S ribosomal protein S14 type Z
+Macromolecule #46: 30S ribosomal protein S15
+Macromolecule #47: 30S ribosomal protein S16
+Macromolecule #48: 30S ribosomal protein S17
+Macromolecule #49: 30S ribosomal protein S18
+Macromolecule #50: 30S ribosomal protein S19
+Macromolecule #51: 30S ribosomal protein S20
+Macromolecule #52: 30S ribosomal protein Thx
+Macromolecule #54: Peptide chain release factor 1
+Macromolecule #56: P-site Peptidyl-tRNA fMEAAAKC-tRNAcys Peptide-part
+Macromolecule #57: MAGNESIUM ION
+Macromolecule #58: POTASSIUM ION
+Macromolecule #59: ZINC ION
+Macromolecule #60: IRON/SULFUR CLUSTER
+Macromolecule #61: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.375 mg/mL |
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Buffer | pH: 7.6 Details: 5 mM HEPES-KOH, 50 mM KCl, 10 mM NH4Cl, 10 mM Mg(CH3COO)2 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Pressure: 0.024 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 295 K / Instrument: LEICA EM GP |
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Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 25104 / Average exposure time: 1.1984 sec. / Average electron dose: 39.7153 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-9no7: |