6OGG

70S termination complex with RF2 bound to the UGA codon. Rotated ribosome with RF2 bound (Structure IV).

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Extensive ribosome and RF2 rearrangements during translation termination.

Svidritskiy, E., Demo, G., Loveland, A.B., Xu, C., Korostelev, A.A.

(2019) Elife 8

  • DOI: 10.7554/eLife.46850
  • Primary Citation of Related Structures:  
    6OGG, 6OGF, 6OGI, 6OG7, 6OFX

  • PubMed 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 ribosome recycling. To visualize termination by RF2, ...

    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 E. coli 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.

    Organizational Affiliation: 

    Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States.



Macromolecules

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50S ribosomal protein L2b273Escherichia coliMutation(s): 0 
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50S ribosomal protein L3c209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4d201Escherichia coliMutation(s): 0 
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50S ribosomal protein L5e179Escherichia coliMutation(s): 0 
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50S ribosomal protein L6f177Escherichia coliMutation(s): 0 
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MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9g149Escherichia coliMutation(s): 0 
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50S ribosomal protein L13j142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14k123Escherichia coliMutation(s): 0 
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50S ribosomal protein L15l144Escherichia coliMutation(s): 0 
Gene Names: 
rplO, A8C65_19395, A9R57_24660, ACU57_21045, AM464_09135, AUQ13_22145, BANRA_01932, BANRA_03684, BHS87_18545, BJJ90_02210, BMA87_18510, BON75_18850, BON98_13310, BUE81_25610, BvCms2454_01416, BvCmsHHP001_00334, BvCmsHHP019_04131, BvCmsHHP056_02703, BvCmsKSP026_02554, BvCmsSINP011_02480, BW690_10710, BZL31_22885, C5F72_02595, C5F73_02860, C5N07_23575, C9E25_20065, C9Z39_20710, CA593_09735, CG692_20270, CI693_13520, CI694_01990, CIG45_22410, D0X26_24495, D2185_22985, D3821_17755, D3O91_20305, D3Y67_24390, D4638_19455, D4718_17880, D9C99_17930, D9D20_21995, D9D44_22490, D9G29_15635, D9G69_20945, D9H68_17710, D9J52_19090, D9Z28_15390, DAH37_14685, DBQ99_03415, DJ503_19770, DL326_22310, DNC98_19095, DT034_22410, DTL43_21000, E2119_19640, E2134_21880, E2135_06185, E4A44_21305, E4K51_21490, E4K55_21420, E4K60_18985, E4K61_20025, E5P22_10480, E5P28_20875, EA213_19860, EAI42_04990, EAI52_16365, EC1094V2_354, EC3234A_55c00230, EC3426_04459, ECTO6_00449, ED307_17010, EEP23_17135, EG808_17075, EI021_21030, EI028_20740, EI032_18995, EI041_20035, EIZ93_12470, EL75_0396, EL79_0415, EL80_0407, ELT20_19170, EPT01_19765, ERS085365_03907, ERS085416_03881, ERS139211_03685, ERS150873_04051, EXX71_21335, EYD11_02080, F1E19_19655, F9040_18095, FRV13_20015, FV293_22465, FWK02_06270, G5632_17770, G5688_20025, GHR40_07050, GKF39_20550, GKF74_18130, GKF86_20070, GKF89_18470, GP671_20580, GP689_20785, GP954_00945, GP979_02005, GQE33_22230, GQE34_14255, GQE64_20420, GQM17_19915, GRW05_09060, GRW27_21285, GRW42_19350, GRW57_03540, GRW80_20585, GRW81_21150, NCTC10963_00456, NCTC11022_03475, NCTC11126_02772, NCTC12650_00710, NCTC13216_01351, NCTC9045_00567, NCTC9062_02686, NCTC9117_00757, NCTC9706_02738, PGD_00585, RK56_021420, SAMEA3472047_03862, SAMEA3472080_04748, SAMEA3484427_04887, SAMEA3484429_04875, SAMEA3752559_00346, SAMEA3753300_02227

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50S ribosomal protein L16m136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17n127Escherichia coliMutation(s): 0 
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50S ribosomal protein L18o117Escherichia coliMutation(s): 0 
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50S ribosomal protein L19p115Escherichia coliMutation(s): 0 
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50S ribosomal protein L20q118Escherichia coliMutation(s): 0 
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50S ribosomal protein L21r103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22s110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23t100Escherichia coliMutation(s): 0 
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50S ribosomal protein L24u104Escherichia coliMutation(s): 0 
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50S ribosomal protein L25v94Escherichia coliMutation(s): 0 
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50S ribosomal protein L27w85Escherichia coliMutation(s): 0 
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50S ribosomal protein L28x78Escherichia coliMutation(s): 0 
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50S ribosomal protein L29y63Escherichia coliMutation(s): 0 
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50S ribosomal protein L30z59Escherichia coliMutation(s): 0 
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50S ribosomal protein L32B57Escherichia coliMutation(s): 0 
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50S ribosomal protein L33C55Escherichia coliMutation(s): 0 
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50S ribosomal protein L34D46Escherichia coliMutation(s): 0 
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50S ribosomal protein L35E65Escherichia coliMutation(s): 0 
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50S ribosomal protein L36F38Escherichia coliMutation(s): 0 
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30S ribosomal protein S2G241Escherichia coliMutation(s): 0 
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30S ribosomal protein S3H233Escherichia coliMutation(s): 0 
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30S ribosomal protein S4I206Escherichia coliMutation(s): 0 
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30S ribosomal protein S5J167Escherichia coliMutation(s): 0 
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30S ribosomal protein S6K131Escherichia coliMutation(s): 0 
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30S ribosomal protein S7L156Escherichia coliMutation(s): 0 
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30S ribosomal protein S8M130Escherichia coliMutation(s): 0 
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30S ribosomal protein S9N130Escherichia coliMutation(s): 0 
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30S ribosomal protein S10O103Escherichia coliMutation(s): 0 
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30S ribosomal protein S11P129Escherichia coliMutation(s): 0 
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30S ribosomal protein S12Q124Escherichia coliMutation(s): 0 
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30S ribosomal protein S13R118Escherichia coliMutation(s): 0 
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30S ribosomal protein S14S101Escherichia coliMutation(s): 0 
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30S ribosomal protein S15T89Escherichia coliMutation(s): 0 
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30S ribosomal protein S16U82Escherichia coliMutation(s): 0 
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30S ribosomal protein S17V84Escherichia coliMutation(s): 0 
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30S ribosomal protein S18W75Escherichia coliMutation(s): 0 
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30S ribosomal protein S19X92Escherichia coliMutation(s): 0 
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30S ribosomal protein S20Y87Escherichia coliMutation(s): 0 
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30S ribosomal protein S21Z71Escherichia coliMutation(s): 0 
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50S ribosomal protein L1a234Escherichia coliMutation(s): 0 
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Peptide chain release factor 28371Escherichia coliMutation(s): 0 
Gene Names: prfB, C4J69_20115
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16S ribosomal RNA31539Escherichia coli
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23S ribosomal RNA12903Escherichia coli
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5S ribosomal RNA2120Escherichia coli
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tRNAfMet577Escherichia coli
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mRNA427synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM107465
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM127094

Revision History 

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2020-01-08
    Changes: Author supporting evidence