1MVR

Decoding Center & Peptidyl transferase center from the X-ray structure of the Thermus thermophilus 70S ribosome, aligned to the low resolution Cryo-EM map of E.coli 70S Ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A cryo-electron microscopic study of ribosome-bound termination factor RF2

Rawat, U.B.Zavialov, A.V.Sengupta, J.Valle, M.Grassucci, R.A.Linde, J.Vestergaard, B.Ehrenberg, M.Frank, J.

(2003) Nature 421: 87-90

  • DOI: 10.1038/nature01224
  • Primary Citation of Related Structures:  1MI6

  • PubMed Abstract: 
  • Protein synthesis takes place on the ribosome, where genetic information carried by messenger RNA is translated into a sequence of amino acids. This process is terminated when a stop codon moves into the ribosomal decoding centre (DC) and is recogniz ...

    Protein synthesis takes place on the ribosome, where genetic information carried by messenger RNA is translated into a sequence of amino acids. This process is terminated when a stop codon moves into the ribosomal decoding centre (DC) and is recognized by a class-1 release factor (RF). RFs have a conserved GGQ amino-acid motif, which is crucial for peptide release and is believed to interact directly with the peptidyl-transferase centre (PTC) of the 50S ribosomal subunit. Another conserved motif of RFs (SPF in RF2) has been proposed to interact directly with stop codons in the DC of the 30S subunit. The distance between the DC and PTC is approximately 73 A. However, in the X-ray structure of RF2, SPF and GGQ are only 23 A apart, indicating that they cannot be at DC and PTC simultaneously. Here we show that RF2 is in an open conformation when bound to the ribosome, allowing GGQ to reach the PTC while still allowing SPF-stop-codon interaction. The results indicate new interpretations of accuracy in termination, and have implications for how the presence of a stop codon in the DC is signalled to PTC.


    Related Citations: 
    • Crystal structure of the ribosome at 5.5 A resolution
      Yusupov, M.M.,Yusupova, G.Z.,Baucom, A.,Lieberman, K.,Earnest, T.N.,Cate, J.H.,Noller, H.
      (2001) Science 292: 883
    • The path of messenger RNA through the ribosome
      Yusupova, G.Z.,Yusupov, M.M.,Cate, J.H.,Noller, H.
      (2001) Cell 106: 233


    Organizational Affiliation

    Howard Hughes Medical Institute, Health Research, Inc., Empire State Plaza, Albany NY 12201-0509, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S12
O
135Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpsL
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN3
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
L
140Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Gene Names: rplK
Find proteins for P29395 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  P29395
Entity ID: 1
MoleculeChainsLengthOrganism
mRNA, triplet codon (A-site)13Escherichia coli K-12
Entity ID: 2
MoleculeChainsLengthOrganism
Helix 34 of 16S rRNAA45Escherichia coli K-12
Entity ID: 3
MoleculeChainsLengthOrganism
Helix 44 of 16S rRNAB96Escherichia coli K-12
Entity ID: 4
MoleculeChainsLengthOrganism
Helix 69 of 23S rRNAC19Escherichia coli K-12
Entity ID: 5
MoleculeChainsLengthOrganism
Helix 89 of 23S rRNAD59Escherichia coli K-12
Entity ID: 6
MoleculeChainsLengthOrganism
Helix 93 of 23S rRNAE27Escherichia coli K-12
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-01
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance