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- PDB-6tg6: Toprim domain of RNase M5 -

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Basic information

Entry
Database: PDB / ID: 6tg6
TitleToprim domain of RNase M5
ComponentsRibonuclease M5
KeywordsHYDROLASE / RNase M5 / RNase / rRNA / 5S rRNA / precursor rRNA / pre-5S rRNA / ribosomal RNA / ribonuclease / catalytic domain / toprim domain
Function / homology
Function and homology information


ribonuclease M5 / ribonuclease M5 activity / rRNA processing / rRNA binding / cytoplasm
Similarity search - Function
Ribonuclease M5 / Ribonuclease M5, C-terminal domain / Domain of unknown function (DUF4093) / Ribonuclease M5-like, TOPRIM domain / Toprim domain / TOPRIM / Toprim domain profile. / TOPRIM domain
Similarity search - Domain/homology
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsOerum, S. / Catala, M. / Tisne, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: Mol Cell / Year: 2020
Title: Structures of B. subtilis Maturation RNases Captured on 50S Ribosome with Pre-rRNAs.
Authors: Stephanie Oerum / Tom Dendooven / Marjorie Catala / Laetitia Gilet / Clément Dégut / Aude Trinquier / Maxime Bourguet / Pierre Barraud / Sarah Cianferani / Ben F Luisi / Ciarán Condon / Carine Tisné /
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 ...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.
History
DepositionNov 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 28, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonuclease M5


Theoretical massNumber of molelcules
Total (without water)12,5281
Polymers12,5281
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.970, 81.100, 29.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ribonuclease M5 / / RNase M5 / Ribosomal RNA terminal maturase M5


Mass: 12528.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: rnmV_1, rnmV, AVP43_02013 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A161UFV3, UniProt: A0A250DVN1*PLUS, ribonuclease M5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 1.4 M sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.297→40.55 Å / Num. obs: 23385 / % possible obs: 98.72 % / Redundancy: 8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0492 / Net I/σ(I): 20.28
Reflection shellResolution: 1.297→1.344 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.76 / Num. unique obs: 2158 / CC1/2: 0.967 / % possible all: 93.34

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model

Resolution: 1.3→40.55 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.04
RfactorNum. reflection% reflectionSelection details
Rfree0.2013 1163 4.99 %RANDOM
Rwork0.1921 ---
obs0.1926 23306 98.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 52.49 Å2 / Biso mean: 18.6157 Å2 / Biso min: 8.32 Å2
Refinement stepCycle: final / Resolution: 1.3→40.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms878 0 0 98 976
Biso mean---27.16 -
Num. residues----116
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3-1.35640.26221370.2381259895
1.3564-1.42790.22571440.2022742100
1.4279-1.51740.19211460.17842763100
1.5174-1.63460.20421450.16922753100
1.6346-1.79910.18231450.17422782100
1.7991-2.05940.18521460.16342772100
2.0594-2.59460.1991490.1921281799
2.5946-40.550.20531510.2063291697

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