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 
  • R-Value Observed: 0.299 

wwPDB Validation   3D Report Full Report


This is version 1.3 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
  • Primary Citation of Related Structures:  
    2D3O

  • 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 proteins L23, L29, and 23S rRNA are disclosed, many of which differ from those found previously for a heterologous bacterial-archaeal TF-ribosome complex ...

    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

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L23B [auth R]95Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RXK0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Go to UniProtKB:  Q9RXK0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RXK0
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24C [auth S]115Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RXJ1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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UniProt GroupQ9RXJ1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L29D [auth W]67Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RXJ4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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UniProt GroupQ9RXJ4
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Trigger FactorE [auth 1]112Deinococcus radioduransMutation(s): 0 
EC: 5.2.1.8
UniProt
Find proteins for Q9RT21 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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UniProt GroupQ9RT21
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S RIBOSOMAL RNAA [auth 0]2880Deinococcus radiodurans
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.299 
  • R-Value Observed: 0.299 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.5α = 90
b = 410.5β = 90
c = 695.2γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-06
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-10-03
    Changes: Data collection, Database references