2D3O

Structure of Ribosome Binding Domain of the Trigger Factor on the 50S ribosomal subunit from D. radiodurans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.299 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Binding Mode of the Trigger Factor on the Ribosome: Implications for Protein Folding and SRP Interaction

Schlunzen, F.Wilson, D.N.Tian, P.Harms, J.M.McInnes, S.J.Hansen, H.A.Albrecht, R.Buerger, J.Wilbanks, S.M.Fucini, P.

(2005) Structure 13: 1685-1694

  • DOI: 10.1016/j.str.2005.08.007

  • PubMed Abstract: 
  • This study presents the X-ray structure of the N-terminal binding domain of the D. radiodurans trigger factor (TF) in complex with the D. radiodurans large ribosomal subunit. At 3.35 A, a complete description of the interactions with ribosomal protei ...

    This study presents the X-ray structure of the N-terminal binding domain of the D. radiodurans trigger factor (TF) in complex with the D. radiodurans large ribosomal subunit. At 3.35 A, a complete description of the interactions with ribosomal proteins L23, L29, and 23S rRNA are disclosed, many of which differ from those found previously for a heterologous bacterial-archaeal TF-ribosome complex. The beta hairpin loop of eubacterial L24, which is shorter in archaeal ribosomes, contacts the TF and severely diminishes the molecular cradle proposed to exist between the TF and ribosome. Bound to the ribosome, TF exposes a hydrophobic crevice large enough to accommodate the nascent polypeptide chain. Superimposition of the full-length TF and the signal-recognition particle (SRP) onto the complex shows that simultaneous cohabitation is possible, in agreement with biochemical data, and suggests a model for the interplay of TF, SRP, and the nascent chain during translation.


    Organizational Affiliation

    Max-Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany. Schluenz@molgen.mpg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L23
R
95Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)Gene Names: rplW
Find proteins for Q9RXK0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Go to UniProtKB:  Q9RXK0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L24
S
115Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)Gene Names: rplX
Find proteins for Q9RXJ1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Go to UniProtKB:  Q9RXJ1
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L29
W
67Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)Gene Names: rpmC
Find proteins for Q9RXJ4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Go to UniProtKB:  Q9RXJ4
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Trigger Factor
1
112Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)Gene Names: tig
EC: 5.2.1.8
Find proteins for Q9RT21 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Go to UniProtKB:  Q9RT21
Entity ID: 1
MoleculeChainsLengthOrganism
23S RIBOSOMAL RNA02880Deinococcus radiodurans
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.299 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 169.500α = 90.00
b = 410.500β = 90.00
c = 695.200γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-12-06
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance