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- PDB-6tnn: Mini-RNase III (Mini-III) bound to 50S ribosome with precursor 23... -

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Basic information

Entry
Database: PDB / ID: 6tnn
TitleMini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNA
Components
  • (50S ribosomal protein ...) x 27
  • 5S rRNA5S ribosomal RNA
  • Mini-ribonuclease 3
  • pre-23S rRNA
KeywordsRIBOSOMAL PROTEIN / Mini-RNase III / Mini-III / complex / ribosome / 50S / RNA maturation / RNA processing / precursor 23S rRNA / pre-23S rRNA / 23S rRNA / L3 / RNase III-like fold / RNase
Function / homology
Function and homology information


positive regulation of rRNA processing / ribonuclease III activity / nucleoid / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA nuclease activity / rRNA processing / large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly ...positive regulation of rRNA processing / ribonuclease III activity / nucleoid / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA nuclease activity / rRNA processing / large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / cytoplasmic translation / transferase activity / tRNA binding / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / DNA binding / RNA binding / cytoplasm
Similarity search - Function
Mini-ribonuclease 3 family / Ribonuclease III domain / Ribonuclease III family / Ribonuclease III domain / Ribonuclease III, endonuclease domain superfamily / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / Ribosomal protein L21, conserved site ...Mini-ribonuclease 3 family / Ribonuclease III domain / Ribonuclease III family / Ribonuclease III domain / Ribonuclease III, endonuclease domain superfamily / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L16 signature 1. / : / Ribosomal protein L10 / Ribosomal protein L10P / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L2, conserved site / Ribosomal protein L2 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / : / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L5, N-terminal / Ribosomal protein L5
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Mini-ribonuclease 3 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Mini-ribonuclease 3 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL13
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 3.07 Å
AuthorsOerum, S. / Dendooven, T. / Gilet, L. / Catala, M. / Degut, C. / Trinquier, A. / Barraud, P. / Luisi, B. / Condon, 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
DepositionDec 9, 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

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Assembly

Deposited unit
b: 50S ribosomal protein L10
H: Mini-ribonuclease 3
I: Mini-ribonuclease 3
U: pre-23S rRNA
V: 5S rRNA
W: 50S ribosomal protein L2
X: 50S ribosomal protein L3
Y: 50S ribosomal protein L4
Z: 50S ribosomal protein L5
a: 50S ribosomal protein L6
c: 50S ribosomal protein L13
d: 50S ribosomal protein L14
e: 50S ribosomal protein L15
f: 50S ribosomal protein L16
g: 50S ribosomal protein L17
h: 50S ribosomal protein L18
i: 50S ribosomal protein L19
j: 50S ribosomal protein L20
k: 50S ribosomal protein L21
l: 50S ribosomal protein L22
m: 50S ribosomal protein L23
n: 50S ribosomal protein L24
o: 50S ribosomal protein L27
p: 50S ribosomal protein L32
q: 50S ribosomal protein L33 1
r: 50S ribosomal protein L34
s: 50S ribosomal protein L35
t: 50S ribosomal protein L36
u: 50S ribosomal protein L28
v: 50S ribosomal protein L29
w: 50S ribosomal protein L30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,381,500255
Polymers1,375,93231
Non-polymers5,568224
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, Components of the 50S particle were identified by electrophoresis followed by band digestion and mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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50S ribosomal protein ... , 27 types, 27 molecules bWXYZacdefghijklmnopqrstuvw

#1: Protein 50S ribosomal protein L10 / / BL5 / Cold acclimatization protein / CAP / Vegetative protein 300 / VEG300


Mass: 18101.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P42923
#5: Protein 50S ribosomal protein L2 / / BL2


Mass: 30335.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P42919
#6: Protein 50S ribosomal protein L3 / / BL3


Mass: 22723.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P42920
#7: Protein 50S ribosomal protein L4 /


Mass: 22424.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P42921
#8: Protein 50S ribosomal protein L5 / / BL6


Mass: 20177.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P12877
#9: Protein 50S ribosomal protein L6 / / BL10


Mass: 19543.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P46898
#10: Protein 50S ribosomal protein L13 /


Mass: 16407.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P70974
#11: Protein 50S ribosomal protein L14 /


Mass: 13175.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P12875
#12: Protein 50S ribosomal protein L15 /


Mass: 15410.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P19946
#13: Protein 50S ribosomal protein L16 /


Mass: 16223.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P14577
#14: Protein 50S ribosomal protein L17 / / BL15 / BL21


Mass: 13774.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P20277
#15: Protein 50S ribosomal protein L18 / / BL16


Mass: 12993.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P46899
#16: Protein 50S ribosomal protein L19 /


Mass: 13416.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: O31742
#17: Protein 50S ribosomal protein L20 /


Mass: 13669.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P55873
#18: Protein 50S ribosomal protein L21 / / BL20


Mass: 11296.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P26908
#19: Protein 50S ribosomal protein L22 /


Mass: 12481.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P42060
#20: Protein 50S ribosomal protein L23 /


Mass: 10978.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P42924
#21: Protein 50S ribosomal protein L24 / / 12 kDa DNA-binding protein / BL23 / HPB12


Mass: 11166.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P0CI78
#22: Protein 50S ribosomal protein L27 / / BL24 / BL30


Mass: 10391.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P05657
#23: Protein 50S ribosomal protein L32 /


Mass: 6745.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: O34687
#24: Protein/peptide 50S ribosomal protein L33 1 / Ribosome


Mass: 5915.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P56849
#25: Protein/peptide 50S ribosomal protein L34 /


Mass: 5271.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P05647
#26: Protein 50S ribosomal protein L35 /


Mass: 7581.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P55874
#27: Protein/peptide 50S ribosomal protein L36 / / BL38 / Ribosomal protein B / Ribosomal protein II


Mass: 4318.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P20278
#28: Protein 50S ribosomal protein L28 /


Mass: 6826.144 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P37807
#29: Protein 50S ribosomal protein L29 /


Mass: 7728.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P12873
#30: Protein 50S ribosomal protein L30 / / BL27


Mass: 6650.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168
References: UniProt: P19947

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Protein , 1 types, 2 molecules HI

#2: Protein Mini-ribonuclease 3 / Mini-RNase 3 / Mini-RNase III / Mini-III


Mass: 16251.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168
Gene: mrnC, yazC, BSU00950 / Production host: Escherichia coli (E. coli)
References: UniProt: O31418, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters

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RNA chain , 2 types, 2 molecules UV

#3: RNA chain pre-23S rRNA


Mass: 950280.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 467326
#4: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 37420.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: GenBank: 1150402534

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Non-polymers , 2 types, 224 molecules

#31: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 221 / Source method: obtained synthetically / Formula: Mg
#32: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Mini-RNase III bound to 50S ribosome with precursor 23S rRNARIBOSOME#1-#300MULTIPLE SOURCES
2Mini-RNase III bound to 50S ribosome with precursor 23S rRNARIBOSOME#1, #3-#301NATURAL
3Mini-RNase III bound to 50S ribosome with precursor 23S rRNARIBOSOME#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Bacillus subtilis subsp. subtilis str. 168 (bacteria)224308
23Bacillus subtilis subsp. subtilis str. 168 (bacteria)224308
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 23.94 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7UCSF Chimera1.11.2model fitting
9PHENIX1.16model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57683 / Symmetry type: POINT
Atomic model buildingPDB-ID: 3J3V

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