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- PDB-6w6v: Structure of yeast RNase MRP holoenzyme -

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Basic information

Entry
Database: PDB / ID: 6w6v
TitleStructure of yeast RNase MRP holoenzyme
Components
  • (Ribonuclease MRP protein subunit ...) x 2
  • (Ribonuclease P/MRP protein subunit ...) x 2
  • (Ribonucleases P/MRP protein subunit ...) x 4
  • RNA component of RNase MRP NME1
  • RNases MRP/P 32.9 kDa subunit
KeywordsHYDROLASE / ribozyme / RNP / ribonucleoprotein
Function / homology
Function and homology information


ribonuclease MRP activity / nuclear-transcribed mRNA catabolic process, RNase MRP-dependent / intronic box C/D snoRNA processing / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / plasmid partitioning / ribonuclease P / nuclease activity ...ribonuclease MRP activity / nuclear-transcribed mRNA catabolic process, RNase MRP-dependent / intronic box C/D snoRNA processing / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / plasmid partitioning / ribonuclease P / nuclease activity / rRNA primary transcript binding / ribonuclease P activity / telomerase holoenzyme complex / tRNA 5'-leader removal / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / tRNA processing / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA processing / rRNA processing / nucleolus / RNA binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / Ribonuclease MRP protein subunit RMP1 / Ribonucleases P/MRP protein subunit Pop8 / : / Ribonucleases P/MRP protein subunit Pop8 / Ribonuclease P/MRP subunit Pop7, fungi / Pop1, N-terminal / POPLD domain / Ribonuclease P/MRP protein subunit Pop5 ...: / : / Ribonuclease MRP protein subunit RMP1 / Ribonucleases P/MRP protein subunit Pop8 / : / Ribonucleases P/MRP protein subunit Pop8 / Ribonuclease P/MRP subunit Pop7, fungi / Pop1, N-terminal / POPLD domain / Ribonuclease P/MRP protein subunit Pop5 / Ribonucleases P/MRP protein subunit Pop1 / Ribonucleases P/MRP protein subunit POP1, N-terminal / POPLD (NUC188) domain / Ribonucleases P/MRP protein subunit Rpp20/Pop7 / Rpp20 subunit of nuclear RNase MRP and P / RNase P subunit Pop5/Rpp14/Rnp2-like / Ribonuclease P/MRP subunit Rpp29 / RNase P subunit Pop5/Rpp14/Rnp2-like domain superfamily / Rpp14/Pop5 family / RNase P subunit p30 / Ribonuclease P subunit, Rpr2/Snm1/Rpp21 / RNase P subunit p30 / RNAse P Rpr2/Rpp21/SNM1 subunit domain / Ribonuclease P protein subunit Rpp29/RNP1 / Ribonuclease P/MRP subunit Rpp29 superfamily / Ribonuclease P/MRP, subunit p29 / A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins. / Rof/RNase P-like / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily / Polymerase/histidinol phosphatase-like
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / Ribonuclease P/MRP protein subunit POP5 / Ribonucleases P/MRP protein subunit POP8 / Ribonucleases P/MRP protein subunit POP7 / RNases MRP/P 32.9 kDa subunit / Ribonuclease P/MRP protein subunit RPP1 / Ribonuclease MRP protein subunit SNM1 ...: / RNA / RNA (> 10) / RNA (> 100) / Ribonuclease P/MRP protein subunit POP5 / Ribonucleases P/MRP protein subunit POP8 / Ribonucleases P/MRP protein subunit POP7 / RNases MRP/P 32.9 kDa subunit / Ribonuclease P/MRP protein subunit RPP1 / Ribonuclease MRP protein subunit SNM1 / Ribonucleases P/MRP protein subunit POP1 / Ribonucleases P/MRP protein subunit POP6 / Ribonuclease MRP protein subunit RMP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsPerederina, A. / Li, D. / Lee, H. / Bator, C. / Berezin, I. / Hafenstein, S.L. / Krasilnikov, A.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM135598 United States
CitationJournal: Nat Commun / Year: 2020
Title: Cryo-EM structure of catalytic ribonucleoprotein complex RNase MRP.
Authors: Anna Perederina / Di Li / Hyunwook Lee / Carol Bator / Igor Berezin / Susan L Hafenstein / Andrey S Krasilnikov /
Abstract: RNase MRP is an essential eukaryotic ribonucleoprotein complex involved in the maturation of rRNA and the regulation of the cell cycle. RNase MRP is related to the ribozyme-based RNase P, but it has ...RNase MRP is an essential eukaryotic ribonucleoprotein complex involved in the maturation of rRNA and the regulation of the cell cycle. RNase MRP is related to the ribozyme-based RNase P, but it has evolved to have distinct cellular roles. We report a cryo-EM structure of the S. cerevisiae RNase MRP holoenzyme solved to 3.0 Å. We describe the structure of this 450 kDa complex, interactions between its components, and the organization of its catalytic RNA. We show that some of the RNase MRP proteins shared with RNase P undergo an unexpected RNA-driven remodeling that allows them to bind to divergent RNAs. Further, we reveal how this RNA-driven protein remodeling, acting together with the introduction of new auxiliary elements, results in the functional diversification of RNase MRP and its progenitor, RNase P, and demonstrate structural underpinnings of the acquisition of new functions by catalytic RNPs.
History
DepositionMar 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: 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 1.2Mar 6, 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: RNA component of RNase MRP NME1
B: Ribonucleases P/MRP protein subunit POP1
D: RNases MRP/P 32.9 kDa subunit
E: Ribonuclease P/MRP protein subunit POP5
F: Ribonucleases P/MRP protein subunit POP6
G: Ribonucleases P/MRP protein subunit POP7
H: Ribonucleases P/MRP protein subunit POP8
I: Ribonuclease P/MRP protein subunit RPP1
J: Ribonuclease P/MRP protein subunit RPP1
K: Ribonuclease MRP protein subunit SNM1
L: Ribonuclease MRP protein subunit RMP1


Theoretical massNumber of molelcules
Total (without water)422,24911
Polymers422,24911
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area50850 Å2
ΔGint-304 kcal/mol
Surface area151550 Å2

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Components

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Ribonucleases P/MRP protein subunit ... , 4 types, 4 molecules BFGH

#2: Protein Ribonucleases P/MRP protein subunit POP1 / RNA-processing protein POP1 / RNases P/MRP 100.4 kDa subunit


Mass: 100559.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P41812, ribonuclease P
#5: Protein Ribonucleases P/MRP protein subunit POP6 / RNA-processing protein POP6 / RNases P/MRP 18.2 kDa subunit


Mass: 18234.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P53218, ribonuclease P
#6: Protein Ribonucleases P/MRP protein subunit POP7 / RNA-processing protein POP7 / RNases P/MRP 15.8 kDa subunit


Mass: 15844.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38291, ribonuclease P
#7: Protein Ribonucleases P/MRP protein subunit POP8 / RNA-processing protein POP8 / RNases P/MRP 15.5 kDa subunit


Mass: 15530.351 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38208, ribonuclease P

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Ribonuclease P/MRP protein subunit ... , 2 types, 3 molecules EIJ

#4: Protein Ribonuclease P/MRP protein subunit POP5 / RNA-processing protein POP5 / RNase P/MRP 19.6 kDa subunit


Mass: 19601.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P28005, ribonuclease P
#8: Protein Ribonuclease P/MRP protein subunit RPP1 / RNA-processing protein RPP1 / RNaseP/MRP 32.2 kDa subunit


Mass: 32270.262 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38786, ribonuclease P

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Ribonuclease MRP protein subunit ... , 2 types, 2 molecules KL

#9: Protein Ribonuclease MRP protein subunit SNM1 / RNA-processing protein SNM1 / RNase MRP 22.5 kDa subunit


Mass: 22578.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P40993
#10: Protein Ribonuclease MRP protein subunit RMP1 / RNA-processing protein RMP1 / RNase MRP 23.6 kDa subunit


Mass: 23657.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q12530

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RNA chain / Protein , 2 types, 2 molecules AD

#1: RNA chain RNA component of RNase MRP NME1 /


Mass: 108767.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / References: GenBank: 4037
#3: Protein RNases MRP/P 32.9 kDa subunit / RNA-processing protein POP4


Mass: 32933.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38336

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Ribonuclease MRP / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.45 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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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 FIELDBright-field microscopy
Image recordingElectron dose: 39 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.1_3865: / Classification: refinement
EM softwareName: PHENIX / Version: 1.18.1 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 155205 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00425915
ELECTRON MICROSCOPYf_angle_d0.60736361
ELECTRON MICROSCOPYf_dihedral_angle_d16.7026038
ELECTRON MICROSCOPYf_chiral_restr0.0414345
ELECTRON MICROSCOPYf_plane_restr0.0043525

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