4KD8: 70s Ribosome Translocation Intermediate Fa-3.6a Containing Elongation Factor Efg/fusidic Acid/gdp, Mrna, And Trna Bound In The Pe*/e State

Citation:
Abstract
Translocation of messenger and transfer RNA (mRNA and tRNA) through the ribosome is a crucial step in protein synthesis, whose mechanism is not yet understood. The crystal structures of three Thermus ribosome-tRNA-mRNA-EF-G complexes trapped with beta,gamma-imidoguanosine 5'-triphosphate (GDPNP) or fusidic acid reveal conformational changes occurring during intermediate states of translocation, including large-scale rotation of the 30S subunit head and body. In all complexes, the tRNA acceptor ends occupy the 50S subunit E site, while their anticodon stem loops move with the head of the 30S subunit to positions between the P and E sites, forming chimeric intermediate states. Two universally conserved bases of 16S ribosomal RNA that intercalate between bases of the mRNA may act as "pawls" of a translocational ratchet. These findings provide new insights into the molecular mechanism of ribosomal translocation.
MMDB ID: 111550
PDB Deposition Date: 2013/4/24
Updated in MMDB: 2013/08
Experimental Method:
x-ray diffraction
Resolution: 3.5  Å
Source Organism:
Thermus thermophilus HB27
Similar Structures:
Merged PDB IDs:4KD8 4KD9 4KDA 4KDB
Asymmetric Unit for 4KD8: 120-meric
Molecular Components in 4KD8
Label Count Molecule
Proteins (108 molecules)
2
30S Ribosomal Protein S2
Molecule annotation
2
30S Ribosomal Protein S3
Molecule annotation
2
30S Ribosomal Protein S4
Molecule annotation
2
30S Ribosomal Protein S5
Molecule annotation
2
30S Ribosomal Protein S6
Molecule annotation
2
30S Ribosomal Protein S7
Molecule annotation
2
30S Ribosomal Protein S8
Molecule annotation
2
30S Ribosomal Protein S9
Molecule annotation
2
30S Ribosomal Protein S10
Molecule annotation
2
30S Ribosomal Protein S11
Molecule annotation
2
30S Ribosomal Protein S12
Molecule annotation
2
30S Ribosomal Protein S13
Molecule annotation
2
30S Ribosomal Protein S14 Type Z
Molecule annotation
2
30S Ribosomal Protein S15
Molecule annotation
2
30S Ribosomal Protein S16
Molecule annotation
2
30S Ribosomal Protein S17
Molecule annotation
2
30S Ribosomal Protein S18
Molecule annotation
2
30S Ribosomal Protein S19
Molecule annotation
2
30S Ribosomal Protein S20
Molecule annotation
2
Elongation Factor G
Molecule annotation
2
50S Ribosomal Protein L1
Molecule annotation
2
50S Ribosomal Protein L2
Molecule annotation
2
50S Ribosomal Protein L3
Molecule annotation
2
50S Ribosomal Protein L4
Molecule annotation
2
50S Ribosomal Protein L5
Molecule annotation
2
50S Ribosomal Protein L6
Molecule annotation
1
50S Ribosomal Protein L10
Molecule annotation
2
50S Ribosomal Protein L11
Molecule annotation
2
50S Ribosomal Protein L13
Molecule annotation
2
50S Ribosomal Protein L14
Molecule annotation
2
50S Ribosomal Protein L15
Molecule annotation
2
50S Ribosomal Protein L16
Molecule annotation
2
50S Ribosomal Protein L17
Molecule annotation
2
50S Ribosomal Protein L18
Molecule annotation
2
50S Ribosomal Protein L19
Molecule annotation
2
50S Ribosomal Protein L20
Molecule annotation
2
50S Ribosomal Protein L21
Molecule annotation
2
50S Ribosomal Protein L22
Molecule annotation
2
50S Ribosomal Protein L23
Molecule annotation
2
50S Ribosomal Protein L24
Molecule annotation
2
50S Ribosomal Protein L25
Molecule annotation
2
50S Ribosomal Protein L27
Molecule annotation
2
50S Ribosomal Protein L29
Molecule annotation
2
50S Ribosomal Protein L30
Molecule annotation
2
50S Ribosomal Protein L32
Molecule annotation
2
50S Ribosomal Protein L33
Molecule annotation
2
50S Ribosomal Protein L34
Molecule annotation
2
50S Ribosomal Protein L35
Molecule annotation
2
50S Ribosomal Protein L36
Molecule annotation
2
50S Ribosomal Protein L7/l12
Molecule annotation
1
50S Ribosomal Protein L7/l12
Molecule annotation
1
50S Ribosomal Protein L7/l12
Molecule annotation
2
50S Ribosomal Protein L28
Molecule annotation
2
50S Ribosomal Protein L31
Molecule annotation
1
50S Ribosomal Protein L10
Molecule annotation
1
50S Ribosomal Protein L7/l12
Molecule annotation
1
50S Ribosomal Protein L7/l12
Molecule annotation
Nucleotides(6 molecules)
2
Ribosomal RNA 16S
Molecule annotation
2
Transfer RNA
Molecule annotation
2
Messenger RNA
Molecule annotation
2
Viomycin
Molecule annotation
2
23S Ribosomal RNA
Molecule annotation
2
5S Ribosomal RNA
Molecule annotation
Chemicals (6 molecules)
1
2
2
2
3
2
* Click molecule labels to explore molecular sequence information.

Citing MMDB
.