PDBsum entry 5eew

RNA binding protein

PDB id: 5eew

Contents

Protein chains

(+ 16 more) 69 a.a.

DNA/RNA

Ligands

TRP ×22

Waters ×743

PDB id:

5eew

Name:

RNA binding protein

Title:

Radiation damage to the trap-RNA complex: dose (dwd) 6.45 mgy

Structure:

Transcription attenuation protein mtrb. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v. Fragment: trp RNA-binding attenuation protein (trap). Synonym: trp RNA-binding attenuation protein,trap,tryptophan RNA- binding attenuator protein. Engineered: yes. (Gaguu)10gag 53-nucleotide RNA. Chain: w.

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422. Gene: mtrb. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630. Other_details: synthetic RNA. In-vitro transcription

Resolution:

1.98Å R-factor: 0.211 R-free: 0.243

Authors:

C.S.Bury,J.E.Mcgeehan,E.F.Garman,M.B.Shevtsov

Key ref:

C.S.Bury et al. (2016). RNA protects a nucleoprotein complex against radiation damage. Acta Crystallogr D Struct Biol, 72, 648-657. PubMed id: 27139628 DOI: 10.1107/S2059798316003351

Date:

23-Oct-15 Release date: 04-May-16

Protein chains

Q9X6J6  (MTRB_GEOSE) -  Transcription attenuation protein MtrB from Geobacillus stearothermophilus

Seq: 74 a.a.

Struc: 69 a.a.

DNA/RNA chain

G-A-G-U-G-A-G-U-G-A-G-U-G-A-G-U-G-A-G-U-G-A-G-U-G-A-G-U-G-A-G-U-G-A-G-U-G-A-G- 44 bases

DOI no: 10.1107/S2059798316003351

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

PubMed id: 27139628

RNA protects a nucleoprotein complex against radiation damage.

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

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-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.