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- PDB-6tgj: RNA-binding domain of RNase M5 -

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Basic information

Entry
Database: PDB / ID: 6tgj
TitleRNA-binding domain of RNase M5
ComponentsRibonuclease M5
KeywordsRNA BINDING PROTEIN / RNase M5 / RNase / rRNA / 5S rRNA / precursor rRNA / pre-5S rRNA / ribosomal RNA / ribonuclease / novel fold / RNA-binding domain
Function / homology
Function and homology information


ribonuclease M5 / ribonuclease M5 activity / rRNA processing / rRNA binding / metal ion binding / cytoplasm
Similarity search - Function
Ribonuclease M5 / Ribonuclease M5, C-terminal domain / Domain of unknown function (DUF4093) / Ribonuclease M5-like, TOPRIM domain / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain
Similarity search - Domain/homology
Ribonuclease M5 / :
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.5 Å
AuthorsOerum, S. / Catala, M. / Degut, C. / 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 30, 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

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease M5
B: Ribonuclease M5


Theoretical massNumber of molelcules
Total (without water)20,4712
Polymers20,4712
Non-polymers00
Water2,162120
1
A: Ribonuclease M5


Theoretical massNumber of molelcules
Total (without water)10,2361
Polymers10,2361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease M5


Theoretical massNumber of molelcules
Total (without water)10,2361
Polymers10,2361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.801, 72.594, 72.985
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 10235.617 Da / Num. of mol.: 2
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: A0A087LGV4*PLUS, ribonuclease M5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 1.8 Å3/Da / Density % sol: 31.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M cacodylate pH 6.5, 0.2 ammonium sulfate and 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.497→36.492 Å / Num. obs: 24152 / % possible obs: 98.1 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04584 / Net I/av σ(I): 20.1 / Net I/σ(I): 20.16
Reflection shellResolution: 1.497→1.551 Å / Rmerge(I) obs: 1.431 / Mean I/σ(I) obs: 1.14 / Num. unique obs: 2249 / CC1/2: 0.565

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.5→36.492 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.76
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 1210 5.01 %RANDOM
Rwork0.2099 ---
obs0.2121 24138 98.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.81 Å2 / Biso mean: 30.1899 Å2 / Biso min: 16.33 Å2
Refinement stepCycle: final / Resolution: 1.5→36.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1104 0 0 122 1226
Biso mean---38.9 -
Num. residues----136
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.55650.36931230.3183236692
1.5565-1.62730.2841090.2792251798
1.6273-1.71310.27391410.2627249199
1.7131-1.82040.34451230.2404254398
1.8204-1.9610.26251540.2441250598
1.961-2.15830.27361190.2214255998
2.1583-2.47050.251450.2132257199
2.4705-3.11240.26681370.21562630100
3.1124-36.4920.22571590.18222746100

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