1MJ1

FITTING THE TERNARY COMPLEX OF EF-Tu/tRNA/GTP AND RIBOSOMAL PROTEINS INTO A 13 A CRYO-EM MAP OF THE COLI 70S RIBOSOME

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Ribosome Interactions of Aminoacyl-tRNA and Elongation Factor TU in the Codon Recognition Complex

Stark, H., Rodnina, M.V., Wieden, H.-J., Zemlin, F., Wintermeyer, W., van Heel, M.

(2002) Nat.Struct.Mol.Biol. 9: 849-854

  • DOI: 10.1038/nsb859

  • PubMed Abstract: 

    • The mRNA codon in the ribosomal A-site is recognized by aminoacyl-tRNA (aa-tRNA) in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Here we report the 13 A resolution three-dimensional reconstruction determined by cryo-electron microscop ...

    The mRNA codon in the ribosomal A-site is recognized by aminoacyl-tRNA (aa-tRNA) in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Here we report the 13 A resolution three-dimensional reconstruction determined by cryo-electron microscopy of the kirromycin-stalled codon-recognition complex. The structure of the ternary complex is distorted by binding of the tRNA anticodon arm in the decoding center. The aa-tRNA interacts with 16S rRNA, helix 69 of 23S rRNA and proteins S12 and L11, while the sarcin-ricin loop of 23S rRNA contacts domain 1 of EF-Tu near the nucleotide-binding pocket. These results provide a detailed snapshot view of an important functional state of the ribosome and suggest mechanisms of decoding and GTPase activation.

    Organizational Affiliation: 

    Max-Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany. holger.stark@mpibpc.mpg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Elongation Factor Tu
A
405Thermus aquaticusMutation(s): 0 
Gene Names: tuf (tufA)
Find proteins for Q01698 (Thermus aquaticus)
Go to UniProtKB:  Q01698
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
S12 ribosomal protein
O
135Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsL
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN3
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
S13 ribosomal protein
P
126Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsM (rps13)
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80377
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
L11 ribosomal protein
L
141Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
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
Phe-tRNAD,C76Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
sarcin-ricin loop of 23SrRNAQ41Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
helix 69 of 23S rRNAR27Escherichia coli
Small Molecules
Modified Residues  11 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
C, D
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
C, D
RNA LINKINGC10 H16 N3 O8 PC
M2G
Query on M2G
C, D
RNA LINKINGC12 H18 N5 O8 PG
1MA
Query on 1MA
C, D
RNA LINKINGC11 H16 N5 O7 PA
OMC
Query on OMC
C, D
RNA LINKINGC10 H16 N3 O8 PC
2MG
Query on 2MG
C, D
RNA LINKINGC11 H16 N5 O8 PG
OMG
Query on OMG
C, D
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
C, D
RNA LINKINGC11 H18 N5 O8 PG
YG
Query on YG
C, D
RNA LINKINGC21 H29 N6 O12 PG
5MU
Query on 5MU
C, D
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
C, D
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
EMrefinement
IMAGIC-5refinement
SITUSrefinement
AMIRArefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-11-01
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2018-07-18
    Type: Data collection