3J5T: Structure Of The Ribosome With Elongation Factor G Trapped In The Pre- Translocation State (pre-translocation 70s*trna Structure, 30s Subunit With Hybrid A/p And P/e Trnas And Viomycin)

Citation:
Abstract
During protein synthesis, tRNAs and their associated mRNA codons move sequentially on the ribosome from the A (aminoacyl) site to the P (peptidyl) site to the E (exit) site in a process catalyzed by a universally conserved ribosome-dependent GTPase [elongation factor G (EF-G) in prokaryotes and elongation factor 2 (EF-2) in eukaryotes]. Although the high-resolution structure of EF-G bound to the posttranslocation ribosome has been determined, the pretranslocation conformation of the ribosome bound with EF-G and A-site tRNA has evaded visualization owing to the transient nature of this state. Here we use electron cryomicroscopy to determine the structure of the 70S ribosome with EF-G, which is trapped in the pretranslocation state using antibiotic viomycin. Comparison with the posttranslocation ribosome shows that the small subunit of the pretranslocation ribosome is rotated by approximately 12 degrees relative to the large subunit. Domain IV of EF-G is positioned in the cleft between the body and head of the small subunit outwardly of the A site and contacts the A-site tRNA. Our findings suggest a model in which domain IV of EF-G promotes the translocation of tRNA from the A to the P site as the small ribosome subunit spontaneously rotates back from the hybrid, rotated state into the nonrotated posttranslocation state.
MMDB ID: 116150
PDB Deposition Date: 2013/11/20
Updated in MMDB: 2014/05
Experimental Method:
electron microscopy
Resolution: 7.6  Å
Source Organism:
Escherichia coli K-12
Similar Structures:
Merged PDB IDs:3J5T 3J5U
Biological Unit for 3J5T: 58-meric
Molecular Components in 3J5T
Label Count Molecule
Proteins (51 molecules)
1
30S Ribosomal Protein S2
Molecule annotation
1
30S Ribosomal Protein S3
Molecule annotation
1
30S Ribosomal Protein S4
Molecule annotation
1
30S Ribosomal Protein S5
Molecule annotation
1
30S Ribosomal Protein S6
Molecule annotation
1
30S Ribosomal Protein S7
Molecule annotation
1
30S Ribosomal Protein S8
Molecule annotation
1
30S Ribosomal Protein S9
Molecule annotation
1
30S Ribosomal Protein S10
Molecule annotation
1
30S Ribosomal Protein S11
Molecule annotation
1
30S Ribosomal Protein S12
Molecule annotation
1
30S Ribosomal Protein S13
Molecule annotation
1
30S Ribosomal Protein S14
Molecule annotation
1
30S Ribosomal Protein S15
Molecule annotation
1
30S Ribosomal Protein S16
Molecule annotation
1
30S Ribosomal Protein S17
Molecule annotation
1
30S Ribosomal Protein S18
Molecule annotation
1
30S Ribosomal Protein S19
Molecule annotation
1
30S Ribosomal Protein S20
Molecule annotation
1
30S Ribosomal Protein S21
Molecule annotation
1
50S Ribosomal Protein L1
Molecule annotation
1
50S Ribosomal Protein L2
Molecule annotation
1
50S Ribosomal Protein L3
Molecule annotation
1
50S Ribosomal Protein L4
Molecule annotation
1
50S Ribosomal Protein L5
Molecule annotation
1
50S Ribosomal Protein L6
Molecule annotation
1
50S Ribosomal Protein L9
Molecule annotation
1
50S Ribosomal Protein L10
Molecule annotation
1
50S Ribosomal Protein L11
Molecule annotation
1
50S Ribosomal Protein L13
Molecule annotation
1
50S Ribosomal Protein L14
Molecule annotation
1
50S Ribosomal Protein L15
Molecule annotation
1
50S Ribosomal Protein L16
Molecule annotation
1
50S Ribosomal Protein L17
Molecule annotation
1
50S Ribosomal Protein L18
Molecule annotation
1
50S Ribosomal Protein L19
Molecule annotation
1
50S Ribosomal Protein L20
Molecule annotation
1
50S Ribosomal Protein L21
Molecule annotation
1
50S Ribosomal Protein L22
Molecule annotation
1
50S Ribosomal Protein L23
Molecule annotation
1
50S Ribosomal Protein L24
Molecule annotation
1
50S Ribosomal Protein L25
Molecule annotation
1
50S Ribosomal Protein L27
Molecule annotation
1
50S Ribosomal Protein L28
Molecule annotation
1
50S Ribosomal Protein L29
Molecule annotation
1
50S Ribosomal Protein L30
Molecule annotation
1
50S Ribosomal Protein L32
Molecule annotation
1
50S Ribosomal Protein L33
Molecule annotation
1
50S Ribosomal Protein L34
Molecule annotation
1
50S Ribosomal Protein L35
Molecule annotation
1
50S Ribosomal Protein L36
Molecule annotation
Nucleotides(6 molecules)
1
16S Ribosomal RNA
Molecule annotation
2
tRNA
Molecule annotation
1
mRNA
Molecule annotation
1
Viomycin
Molecule annotation
1
23S Ribosomal RNA
Molecule annotation
1
5S Ribosomal RNA
Molecule annotation
Chemical (1 molecule)
1
1
* Click molecule labels to explore molecular sequence information.

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