2OM7

Structural Basis for Interaction of the Ribosome with the Switch Regions of GTP-bound Elongation Factors


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.3 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

Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors.

Connell, S.R.Takemoto, C.Wilson, D.N.Wang, H.Murayama, K.Terada, T.Shirouzu, M.Rost, M.Schuler, M.Giesebrecht, J.Dabrowski, M.Mielke, T.Fucini, P.Yokoyama, S.Spahn, C.M.

(2007) Mol.Cell 25: 751-764

  • DOI: 10.1016/j.molcel.2007.01.027

  • PubMed Abstract: 
  • Elongation factor G (EF-G) catalyzes tRNA translocation on the ribosome. Here a cryo-EM reconstruction of the 70S*EF-G ribosomal complex at 7.3 A resolution and the crystal structure of EF-G-2*GTP, an EF-G homolog, at 2.2 A resolution are presented. ...

    Elongation factor G (EF-G) catalyzes tRNA translocation on the ribosome. Here a cryo-EM reconstruction of the 70S*EF-G ribosomal complex at 7.3 A resolution and the crystal structure of EF-G-2*GTP, an EF-G homolog, at 2.2 A resolution are presented. EF-G-2*GTP is structurally distinct from previous EF-G structures, and in the context of the cryo-EM structure, the conformational changes are associated with ribosome binding and activation of the GTP binding pocket. The P loop and switch II approach A2660-A2662 in helix 95 of the 23S rRNA, indicating an important role for these conserved bases. Furthermore, the ordering of the functionally important switch I and II regions, which interact with the bound GTP, is dependent on interactions with the ribosome in the ratcheted conformation. Therefore, a network of interaction with the ribosome establishes the active GTP conformation of EF-G and thus facilitates GTP hydrolysis and tRNA translocation.


    Organizational Affiliation

    Institut f├╝r Medizinische Physik und Biophysik, Charite-Universit├Ątsmedizin Berlin, Ziegelstrasse 5-9, 10117 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
E
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: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
K
229Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplA
Find proteins for Q5SLP7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP7
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Elongation factor G
L
691Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: fusA (fus)
Find proteins for Q5SHN5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN5
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
N
256Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsB (rps2)
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80371
Entity ID: 1
MoleculeChainsLengthOrganism
Fragment of 16S rRNA (h14)A12Thermus thermophilus
Entity ID: 2
MoleculeChainsLengthOrganism
Fragment of 16S rRNA (h15)B28Thermus thermophilus
Entity ID: 3
MoleculeChainsLengthOrganism
Fragment of 16S rRNA (h44)C96Thermus thermophilus
Entity ID: 4
MoleculeChainsLengthOrganism
16S ribosomal RNA (H5)D303Thermus thermophilus
Entity ID: 5
MoleculeChainsLengthOrganism
Fragment of23S rRNA (H95)F29Thermus thermophilus
Entity ID: 6
MoleculeChainsLengthOrganism
Fragment of23S rRNA (H68)G54Thermus thermophilus
Entity ID: 7
MoleculeChainsLengthOrganism
Fragment of23S rRNA (H89)H42Thermus thermophilus
Entity ID: 8
MoleculeChainsLengthOrganism
Fragment of23S rRNA (H42-44)I58Thermus thermophilus
Entity ID: 9
MoleculeChainsLengthOrganism
Fragment of23S rRNA (H76)J102Thermus thermophilus
Entity ID: 10
MoleculeChainsLengthOrganism
p/E-tRNAM74Thermus thermophilus
Small Molecules
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
M
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
M
RNA LINKINGC10 H16 N3 O8 PC
4SU
Query on 4SU
M
RNA LINKINGC9 H13 N2 O8 P SU
5MU
Query on 5MU
M
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
M
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
SPIDERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-03-12
    Type: Derived calculations
  • Version 1.3: 2018-07-18
    Type: Data collection, Database references