5LYB

Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn

This is a non-PDB format compatible entry.

Summary for 5LYB

• Entry DOI: 10.2210/pdb5lyb/pdb
• Descriptor: 18S rRNA, 40S ribosomal protein S8-A, 40S ribosomal protein S9-A, ... (93 entities in total)
• Functional Keywords: ribosome, translation, protein synthesis, proline, aminoacyl-trna, peptide bond formation, catalysis, cyclic amino acids
• Biological source: Saccharomyces cerevisiae (Baker's yeast); More
• Cellular location: Cytoplasm : P0CX39 O13516 P48589 P05756 P06367 Q01855 B3LI22 P0CX51 P02407 P0CX55 P07280 P38701 P0C0V8 P0C0W1 P0CX31 Q3E792 B3RHV0 P39939 P35997 Q3E7X9 P41057 P0CX33 P38011 P25443 P0CX45 P14126 P10664 P26321 Q02326 P05737 P17076 P05738 P05750 P41805 Q3E757 Q12690 P36105 P05748 P26784 P05740 P0CX49 P0CX82 P0CX23 P0CX35 Q02753 P05749 P0CX41 P04449 P04456 P05743 P0C2H6 P02406 P05747 P14120 P26783 P0C2H8 P38061 P05744 P87262 P0CX84 P05745 P49166 P49167 P04650 P0CX37 P0CX86 P0CX27 P0CX25 Q01855 P38011 P26786 P04449; Ubiquitin: Cytoplasm . 40S ribosomal protein S31: Cytoplasm : P05759; Ubiquitin: Cytoplasm . 60S ribosomal protein L40: Cytoplasm: P0CH08
• Total number of polymer chains: 164
• Total formula weight: 6570441.66

Authors

Melnikov, S.,Mailliot, J. (deposition date: 2016-09-26, release date: 2016-11-23, Last modification date: 2024-10-16)

Primary citation

Melnikov, S.,Mailliot, J.,Rigger, L.,Neuner, S.,Shin, B.S.,Yusupova, G.,Dever, T.E.,Micura, R.,Yusupov, M.
Molecular insights into protein synthesis with proline residues.
EMBO Rep., 17:1776-1784, 2016

PubMed Abstract: Proline is an amino acid with a unique cyclic structure that facilitates the folding of many proteins, but also impedes the rate of peptide bond formation by the ribosome. As a ribosome substrate, proline reacts markedly slower when compared with other amino acids both as a donor and as an acceptor of the nascent peptide. Furthermore, synthesis of peptides with consecutive proline residues triggers ribosome stalling. Here, we report crystal structures of the eukaryotic ribosome bound to analogs of mono- and diprolyl-tRNAs. These structures provide a high-resolution insight into unique properties of proline as a ribosome substrate. They show that the cyclic structure of proline residue prevents proline positioning in the amino acid binding pocket and affects the nascent peptide chain position in the ribosomal peptide exit tunnel. These observations extend current knowledge of the protein synthesis mechanism. They also revise an old dogma that amino acids bind the ribosomal active site in a uniform way by showing that proline has a binding mode distinct from other amino acids.

PubMed: 27827794
DOI: 10.15252/embr.201642943

Experimental method

X-RAY DIFFRACTION (3.25 Å)