6TGJ

RNA-binding domain of RNase M5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.252 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of B. subtilis Maturation RNases Captured on 50S Ribosome with Pre-rRNAs.

Oerum, S.Dendooven, T.Catala, M.Gilet, L.Degut, C.Trinquier, A.Bourguet, M.Barraud, P.Cianferani, S.Luisi, B.F.Condon, C.Tisne, C.

(2020) Mol Cell 80: 227

  • DOI: https://doi.org/10.1016/j.molcel.2020.09.008
  • Primary Citation of Related Structures:  
    6TG6, 6TGJ, 6TNN, 6TPQ

  • PubMed Abstract: 

    The pathways for ribosomal RNA (rRNA) maturation diverge greatly among the domains of life. In the Gram-positive model bacterium, Bacillus subtilis, the final maturation steps of the two large ribosomal subunit (50S) rRNAs, 23S and 5S pre-rRNAs, are catalyzed by the double-strand specific ribonucleases (RNases) Mini-RNase III and RNase M5, respectively. Here we present a protocol that allowed us to solve the 3.0 and 3.1 Å resolution cryoelectron microscopy structures of these RNases poised to cleave their pre-rRNA substrates within the B. subtilis 50S particle. These data provide the first structural insights into rRNA maturation in bacteria by revealing how these RNases recognize and process double-stranded pre-rRNA. Our structures further uncover how specific ribosomal proteins act as chaperones to correctly fold the pre-rRNA substrates and, for Mini-III, anchor the RNase to the ribosome. These r-proteins thereby serve a quality-control function in the process from accurate ribosome assembly to rRNA processing.


  • Organizational Affiliation

    Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease M5
A, B
90Geobacillus stearothermophilusMutation(s): 0 
Gene Names: rnmV_1rnmVAVP43_02013
EC: 3.1.26.8
UniProt
Find proteins for A0A087LGV4 (Geobacillus stearothermophilus)
Explore A0A087LGV4 
Go to UniProtKB:  A0A087LGV4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A087LGV4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.801α = 90
b = 72.594β = 90
c = 72.985γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
Arcimboldophasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2020-10-14
    Changes: Database references
  • Version 1.2: 2020-10-28
    Changes: Database references
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references