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- PDB-6of2: Precursor ribosomal RNA processing complex, State 2. -

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Basic information

Entry
Database: PDB / ID: 6of2
TitlePrecursor ribosomal RNA processing complex, State 2.
Components
  • CLP1_P domain-containing protein
  • Ribonuclease
KeywordsRNA BINDING PROTEIN / Complex / Ribonuclease / Polynucleotide kinase
Function / homology
Function and homology information


polynucleotide 5'-hydroxyl-kinase activity / Las1 complex / RNA processing / rRNA processing / endonuclease activity / ATP binding
Similarity search - Function
Las1 / Las1-like / Polyribonucleotide 5'-hydroxyl-kinase Clp1, P-loop domain / Polyribonucleotide 5-hydroxyl-kinase Clp1/Grc3 / mRNA cleavage and polyadenylation factor CLP1 P-loop / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Polynucleotide 5'-hydroxyl-kinase GRC3 / Uncharacterized protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsPillon, M.C. / Hsu, A.L. / Krahn, J.M. / Williams, J.G. / Goslen, K.H. / Sobhany, M. / Borgnia, M.J. / Stanley, R.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIA ES103247 United States
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Cryo-EM reveals active site coordination within a multienzyme pre-rRNA processing complex.
Authors: Monica C Pillon / Allen L Hsu / Juno M Krahn / Jason G Williams / Kevin H Goslen / Mack Sobhany / Mario J Borgnia / Robin E Stanley /
Abstract: Ribosome assembly is a complex process reliant on the coordination of trans-acting enzymes to produce functional ribosomal subunits and secure the translational capacity of cells. The ...Ribosome assembly is a complex process reliant on the coordination of trans-acting enzymes to produce functional ribosomal subunits and secure the translational capacity of cells. The endoribonuclease (RNase) Las1 and the polynucleotide kinase (PNK) Grc3 assemble into a multienzyme complex, herein designated RNase PNK, to orchestrate processing of precursor ribosomal RNA (rRNA). RNase PNK belongs to the functionally diverse HEPN nuclease superfamily, whose members rely on distinct cues for nuclease activation. To establish how RNase PNK coordinates its dual enzymatic activities, we solved a series of cryo-EM structures of Chaetomium thermophilum RNase PNK in multiple conformational states. The structures reveal that RNase PNK adopts a butterfly-like architecture, harboring a composite HEPN nuclease active site flanked by discrete RNA kinase sites. We identify two molecular switches that coordinate nuclease and kinase function. Together, our structures and corresponding functional studies establish a new mechanism of HEPN nuclease activation essential for ribosome production.
History
DepositionMar 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Ribonuclease
B: CLP1_P domain-containing protein
D: Ribonuclease
E: CLP1_P domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,1028
Polymers227,0074
Non-polymers1,0954
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Ribonuclease


Mass: 43842.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0066080 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SGE9
#2: Protein CLP1_P domain-containing protein


Mass: 69660.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0016120 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S263
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestY

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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

ComponentName: Precursor Ribosomal RNA Processing Complex / Type: COMPLEX
Details: Precursor Ribosomal RNA Processing Complex coordinates removal of a transcribed spacer.
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.234 MDa / Experimental value: NO
Source (natural)Organism: Chaetomium thermophilum (fungus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70561 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00611364
ELECTRON MICROSCOPYf_angle_d0.96515520
ELECTRON MICROSCOPYf_dihedral_angle_d11.1036772
ELECTRON MICROSCOPYf_chiral_restr0.051736
ELECTRON MICROSCOPYf_plane_restr0.0071980

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