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- EMDB-20057: 70S termination complex with RF2 bound to the UGA codon. Rotated ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20057 | |||||||||
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Title | 70S termination complex with RF2 bound to the UGA codon. Rotated ribosome with RF2 bound (Structure IV). | |||||||||
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![]() | Ribosome recycling / translation termination / RF2 / intersubunit rotation / RIBOSOME | |||||||||
Function / homology | ![]() translation release factor activity, codon specific / positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / regulation of cell growth / large ribosomal subunit / ribosome binding ...translation release factor activity, codon specific / positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / regulation of cell growth / large ribosomal subunit / ribosome binding / regulation of translation / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
![]() | Svidritskiy E / Demo G / Loveland AB / Xu C / Korostelev AA | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Extensive ribosome and RF2 rearrangements during translation termination. Authors: Egor Svidritskiy / Gabriel Demo / Anna B Loveland / Chen Xu / Andrei A Korostelev / ![]() Abstract: Protein synthesis ends when a ribosome reaches an mRNA stop codon. Release factors (RFs) decode the stop codon, hydrolyze peptidyl-tRNA to release the nascent protein, and then dissociate to allow ...Protein synthesis ends when a ribosome reaches an mRNA stop codon. Release factors (RFs) decode the stop codon, hydrolyze peptidyl-tRNA to release the nascent protein, and then dissociate to allow ribosome recycling. To visualize termination by RF2, we resolved a cryo-EM ensemble of 70S•RF2 structures at up to 3.3 Å in a single sample. Five structures suggest a highly dynamic termination pathway. Upon peptidyl-tRNA hydrolysis, the CCA end of deacyl-tRNA departs from the peptidyl transferase center. The catalytic GGQ loop of RF2 is rearranged into a long β-hairpin that plugs the peptide tunnel, biasing a nascent protein toward the ribosome exit. Ribosomal intersubunit rotation destabilizes the catalytic RF2 domain on the 50S subunit and disassembles the central intersubunit bridge B2a, resulting in RF2 departure. Our structures visualize how local rearrangements and spontaneous inter-subunit rotation poise the newly-made protein and RF2 to dissociate in preparation for ribosome recycling. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 107.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 66.3 KB 66.3 KB | Display Display | ![]() |
Images | ![]() | 243.7 KB | ||
Filedesc metadata | ![]() | 13.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6oggMC ![]() 6ofxC ![]() 6og7C ![]() 6ogfC ![]() 6ogiC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.334 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : tRNAfMet and RF2 bound to a rotated E. coli ribosome
+Supramolecule #1: tRNAfMet and RF2 bound to a rotated E. coli ribosome
+Macromolecule #1: 50S ribosomal protein L2
+Macromolecule #2: 50S ribosomal protein L3
+Macromolecule #3: 50S ribosomal protein L4
+Macromolecule #4: 50S ribosomal protein L5
+Macromolecule #5: 50S ribosomal protein L6
+Macromolecule #6: 50S ribosomal protein L9
+Macromolecule #7: 50S ribosomal protein L13
+Macromolecule #8: 50S ribosomal protein L14
+Macromolecule #9: 50S ribosomal protein L15
+Macromolecule #10: 50S ribosomal protein L16
+Macromolecule #11: 50S ribosomal protein L17
+Macromolecule #12: 50S ribosomal protein L18
+Macromolecule #13: 50S ribosomal protein L19
+Macromolecule #14: 50S ribosomal protein L20
+Macromolecule #15: 50S ribosomal protein L21
+Macromolecule #16: 50S ribosomal protein L22
+Macromolecule #17: 50S ribosomal protein L23
+Macromolecule #18: 50S ribosomal protein L24
+Macromolecule #19: 50S ribosomal protein L25
+Macromolecule #20: 50S ribosomal protein L27
+Macromolecule #21: 50S ribosomal protein L28
+Macromolecule #22: 50S ribosomal protein L29
+Macromolecule #23: 50S ribosomal protein L30
+Macromolecule #24: 50S ribosomal protein L32
+Macromolecule #25: 50S ribosomal protein L33
+Macromolecule #26: 50S ribosomal protein L34
+Macromolecule #27: 50S ribosomal protein L35
+Macromolecule #28: 50S ribosomal protein L36
+Macromolecule #29: 30S ribosomal protein S2
+Macromolecule #30: 30S ribosomal protein S3
+Macromolecule #31: 30S ribosomal protein S4
+Macromolecule #32: 30S ribosomal protein S5
+Macromolecule #33: 30S ribosomal protein S6
+Macromolecule #34: 30S ribosomal protein S7
+Macromolecule #35: 30S ribosomal protein S8
+Macromolecule #36: 30S ribosomal protein S9
+Macromolecule #37: 30S ribosomal protein S10
+Macromolecule #38: 30S ribosomal protein S11
+Macromolecule #39: 30S ribosomal protein S12
+Macromolecule #40: 30S ribosomal protein S13
+Macromolecule #41: 30S ribosomal protein S14
+Macromolecule #42: 30S ribosomal protein S15
+Macromolecule #43: 30S ribosomal protein S16
+Macromolecule #44: 30S ribosomal protein S17
+Macromolecule #45: 30S ribosomal protein S18
+Macromolecule #46: 30S ribosomal protein S19
+Macromolecule #47: 30S ribosomal protein S20
+Macromolecule #48: 30S ribosomal protein S21
+Macromolecule #49: 50S ribosomal protein L1
+Macromolecule #55: Peptide chain release factor 2
+Macromolecule #50: 16S ribosomal RNA
+Macromolecule #51: 23S ribosomal RNA
+Macromolecule #52: 5S ribosomal RNA
+Macromolecule #53: tRNAfMet
+Macromolecule #54: mRNA
-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 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 29.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5881 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |