5EF3

RADIATION DAMAGE TO THE TRAP-RNA COMPLEX: DOSE (DWD) 25.0 MGy


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

RNA protects a nucleoprotein complex against radiation damage.

Bury, C.S.McGeehan, J.E.Antson, A.A.Carmichael, I.Gerstel, M.Shevtsov, M.B.Garman, E.F.

(2016) Acta Crystallogr D Struct Biol 72: 648-657

  • DOI: 10.1107/S2059798316003351
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Radiation damage during macromolecular X-ray crystallographic data collection is still the main impediment for many macromolecular structure determinations. Even when an eventual model results from the crystallographic pipeline, the manifestations of ...

    Radiation damage during macromolecular X-ray crystallographic data collection is still the main impediment for many macromolecular structure determinations. Even when an eventual model results from the crystallographic pipeline, the manifestations of radiation-induced structural and conformation changes, the so-called specific damage, within crystalline macromolecules can lead to false interpretations of biological mechanisms. Although this has been well characterized within protein crystals, far less is known about specific damage effects within the larger class of nucleoprotein complexes. Here, a methodology has been developed whereby per-atom density changes could be quantified with increasing dose over a wide (1.3-25.0 MGy) range and at higher resolution (1.98 Å) than the previous systematic specific damage study on a protein-DNA complex. Specific damage manifestations were determined within the large trp RNA-binding attenuation protein (TRAP) bound to a single-stranded RNA that forms a belt around the protein. Over a large dose range, the RNA was found to be far less susceptible to radiation-induced chemical changes than the protein. The availability of two TRAP molecules in the asymmetric unit, of which only one contained bound RNA, allowed a controlled investigation into the exact role of RNA binding in protein specific damage susceptibility. The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule. Additionally, the method enabled a quantification of the reduction in radiation-induced Lys and Phe disordering upon RNA binding directly from the electron density.


    Related Citations: 
    • Specificity of TRAP-RNA interactions: crystal structures of two complexes with different RNA sequences
      Hopcroft, N.H.,Wendt, A.L.,Gollnick, P.,Antson, A.A.
      (2002) Acta Crystallogr D Biol Crystallogr. 58: 615


    Organizational Affiliation

    Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcription attenuation protein MtrB
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
74Geobacillus stearothermophilusMutation(s): 0 
Gene Names: mtrB
Find proteins for Q9X6J6 (Geobacillus stearothermophilus)
Go to UniProtKB:  Q9X6J6
Entity ID: 2
MoleculeChainsLengthOrganism
(GAGUU)10GAG 53-NUCLEOTIDE RNAW55synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRP
Query on TRP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.239 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 141.230α = 90.00
b = 111.160β = 117.37
c = 138.290γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited Kingdom--

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-05-11
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Data collection