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- PDB-6ah3: Cryo-EM structure of yeast Ribonuclease P with pre-tRNA substrate -

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Basic information

Entry
Database: PDB / ID: 6ah3
TitleCryo-EM structure of yeast Ribonuclease P with pre-tRNA substrate
Components
  • (Ribonuclease P ...) x 2
  • (Ribonuclease P/MRP protein subunit ...) x 2
  • (Ribonucleases P/MRP protein subunit ...) x 5
  • RNases MRP/P 32.9 kDa subunit
  • pre-tRNA
KeywordsHYDROLASE/RNA / Ribonuclease P / RNA-protein complex / HYDROLASE-RNA complex
Function / homologyRibonucleases P/MRP protein subunit Rpp20 / Ribonucleases P/MRP protein subunit Pop8 / Ribonucleases P/MRP protein subunit Pop6 / Ribonuclease P/MRP, p29 subunit / Ribonuclease P/MRP protein subunit Pop5 / Polymerase/histidinol phosphatase-like / RNase P, subunit Pop3 / POPLD domain / Pop1, N-terminal / RNAse P, Rpr2/Rpp21 subunit ...Ribonucleases P/MRP protein subunit Rpp20 / Ribonucleases P/MRP protein subunit Pop8 / Ribonucleases P/MRP protein subunit Pop6 / Ribonuclease P/MRP, p29 subunit / Ribonuclease P/MRP protein subunit Pop5 / Polymerase/histidinol phosphatase-like / RNase P, subunit Pop3 / POPLD domain / Pop1, N-terminal / RNAse P, Rpr2/Rpp21 subunit / DNA/RNA-binding protein Alba-like / Ribonuclease P/MRP protein subunit / RNase P subunit p30 / Ribonuclease P/MRP, subunit p29 / Rof/RNase P-like / Alba-like domain superfamily / Ribonuclease P/MRP, subunit POP7 / Rpp20 subunit of nuclear RNase MRP and P / Rnp2-like domain superfamily / Ribonucleases P/MRP protein subunit Pop1 / Domain of unknown function UPF0086 / RNase P subunit p30 / Rpp14/Pop5 family / Alba / Ribonuclease P/MRP, subunit p29 superfamily / RNAse P Rpr2/Rpp21/SNM1 subunit domain / Ribonucleases P/MRP protein subunit POP1 / POPLD (NUC188) domain / RNase P subunit Pop3 / ribonuclease MRP activity / intronic box C/D snoRNA processing / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay / rRNA primary transcript binding / ribonuclease P / protein lipoylation / telomerase holoenzyme complex / RNA phosphodiester bond hydrolysis, endonucleolytic / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing / mRNA cleavage / ribonuclease activity / rRNA processing / RNA binding / nucleus / metal ion binding / cytosol / cytoplasm / 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 P protein subunit RPR2 / Ribonucleases P/MRP protein subunit POP1 / Ribonucleases P/MRP protein subunit POP6 / Ribonucleases P/MRP protein subunit POP3 / gb:1163001456:
Function and homology information
Specimen sourceSaccharomyces cerevisiae S288c (yeast)
Saccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.48 Å resolution
AuthorsLan, P. / Tan, M. / Wu, J. / Lei, M.
CitationJournal: Science / Year: 2018
Title: Structural insight into precursor tRNA processing by yeast ribonuclease P.
Authors: Pengfei Lan / Ming Tan / Yuebin Zhang / Shuangshuang Niu / Juan Chen / Shaohua Shi / Shuwan Qiu / Xuejuan Wang / Xiangda Peng / Gang Cai / Hong Cheng / Jian Wu / Guohui Li / Ming Lei
Abstract: Ribonuclease P (RNase P) is a universal ribozyme responsible for processing the 5'-leader of pre-transfer RNA (pre-tRNA). Here, we report the 3.5-angstrom cryo-electron microscopy structures of ...Ribonuclease P (RNase P) is a universal ribozyme responsible for processing the 5'-leader of pre-transfer RNA (pre-tRNA). Here, we report the 3.5-angstrom cryo-electron microscopy structures of RNase P alone and in complex with pre-tRNA The protein components form a hook-shaped architecture that wraps around the RNA and stabilizes RNase P into a "measuring device" with two fixed anchors that recognize the L-shaped pre-tRNA. A universally conserved uridine nucleobase and phosphate backbone in the catalytic center together with the scissile phosphate and the O3' leaving group of pre-tRNA jointly coordinate two catalytic magnesium ions. Binding of pre-tRNA induces a conformational change in the catalytic center that is required for catalysis. Moreover, simulation analysis suggests a two-metal-ion S2 reaction pathway of pre-tRNA cleavage. These results not only reveal the architecture of yeast RNase P but also provide a molecular basis of how the 5'-leader of pre-tRNA is processed by eukaryotic RNase P.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 16, 2018 / Release: Oct 17, 2018

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Structure visualization

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Assembly

Deposited unit
A: Ribonuclease P RNA
B: Ribonucleases P/MRP protein subunit POP1
C: Ribonucleases P/MRP protein subunit POP3
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 P protein subunit RPR2
T: pre-tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)451,06515
Polyers450,95112
Non-polymers1143
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Ribonuclease P ... , 2 types, 2 molecules AK

#1: RNA chain Ribonuclease P RNA


Mass: 118857.781 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Details: cell / Strain: ATCC 204508 / S288c / References: GenBank: 1163001456
#10: Protein/peptide Ribonuclease P protein subunit RPR2 / / RNA-processing protein RPR2 / RNase P 16.4 kDa subunit


Mass: 16375.049 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Details: cell / Strain: ATCC 204508 / S288c / References: UniProt: P40571, ribonuclease P

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Ribonucleases P/MRP protein subunit ... , 5 types, 5 molecules BCFGH

#2: Protein/peptide 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: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Details: cell / Strain: ATCC 204508 / S288c / References: UniProt: P41812, ribonuclease P
#3: Protein/peptide Ribonucleases P/MRP protein subunit POP3 / RNA-processing protein POP3 / RNases MRP/P 22.6 kDa subunit


Mass: 22643.721 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Details: cell / Strain: ATCC 204508 / S288c / References: UniProt: P53833
#6: Protein/peptide 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: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Details: cell / Strain: ATCC 204508 / S288c / References: UniProt: P53218, ribonuclease P
#7: Protein/peptide 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: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Details: cell / Strain: ATCC 204508 / S288c / References: UniProt: P38291, ribonuclease P
#8: Protein/peptide 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: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Details: cell / Strain: ATCC 204508 / S288c / References: UniProt: P38208, ribonuclease P

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

#5: Protein/peptide 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: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Details: cell / Strain: ATCC 204508 / S288c / References: UniProt: P28005, ribonuclease P
#9: Protein/peptide 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: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Details: cell / Strain: ATCC 204508 / S288c / References: UniProt: P38786, ribonuclease P

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Protein/peptide / RNA chain , 2 types, 2 molecules DT

#11: RNA chain pre-tRNA


Mass: 25830.324 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Details: in vitro transcription / Plasmid name: pGlms / Production host: Saccharomyces cerevisiae (baker's yeast)
#4: Protein/peptide RNases MRP/P 32.9 kDa subunit / RNA-processing protein POP4


Mass: 32933.168 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Details: cell / Strain: ATCC 204508 / S288c / References: UniProt: P38336

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Non-polymers , 2 types, 3 molecules

#12: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#13: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1RNase P with pre-tRNA substrateCOMPLEX1,2,3,4,5,6,7,8,9,10,110MULTIPLE SOURCES
2RNase PCOMPLEX1,2,3,4,5,6,7,8,9,101NATURAL
3pre-tRNACOMPLEX111RECOMBINANT
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
22559292Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
33559292Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (baker's yeast) / Plasmid: pGlms
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.5625 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 176896 / Symmetry type: POINT

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