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PDBsum entry 3i9d

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Top Page protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome PDB id
3i9d
Jmol
Contents
Protein chains
237 a.a.
205 a.a.
208 a.a.
151 a.a.
101 a.a.
155 a.a.
138 a.a.
127 a.a.
99 a.a.
119 a.a.
125 a.a.
121 a.a.
60 a.a.
88 a.a.
84 a.a.
100 a.a.
70 a.a.
84 a.a.
99 a.a.
25 a.a.
DNA/RNA
Ligands
__G-__G-__G-__U
__G ×5
__G-__A-__G
__C-__A-__G-__C-
__C-__C-__G
__G-__U-__A-__G
__C ×2
__U
__C-__G-__U
__G-__C-__U-__C
__A-__U-__A
__A
__C-__C-__C
__G-__A-__A-__G
__U-__C
__G-__U
__C-__G
__U-__U-__C
__A-__A-__A-__U-
__C-__C-__G-__G-
__C-__C-__C-__C
Metals
_MG
_ZN

References listed in PDB file
Key reference
Title Structural aspects of messenger RNA reading frame maintenance by the ribosome.
Authors L.Jenner, G.Yusupova, M.Yusupov.
Ref. Nat.Struct.Mol.Biol., 2010, 17, 555-560.
PubMed id 20400952
Abstract
One key question in protein biosynthesis is how the ribosome couples mRNA and tRNA movements to prevent disruption of weak codon-anticodon interactions and loss of the translational reading frame during translocation. Here we report the complete path of mRNA on the 70S ribosome at the atomic level (3.1-A resolution), and we show that one of the conformational rearrangements that occurs upon transition from initiation to elongation is a narrowing of the downstream mRNA tunnel. This rearrangement triggers formation of a network of interactions between the mRNA downstream of the A-site codon and the elongating ribosome. Our data elucidate the mechanism by which hypermodified nucleoside 2-methylthio-N6 isopentenyl adenosine at position 37 (ms(2)i(6)A37) in tRNA(Phe)(GAA) stabilizes mRNA-tRNA interactions in all three tRNA binding sites. Another network of contacts is formed between this tRNA modification and ribosomal elements surrounding the mRNA E/P kink, resulting in the anchoring of P-site tRNA. These data allow rationalization of how modification deficiencies of ms(2)i(6)A37 in tRNAs may lead to shifts of the translational reading frame.
PROCHECK
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