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- PDB-6agb: Cryo-EM structure of yeast Ribonuclease P -

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Basic information

Entry
Database: PDB / ID: 6agb
TitleCryo-EM structure of yeast Ribonuclease P
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
KeywordsHYDROLASE/RNA / Ribonuclease P / RNA-protein complex / HYDROLASE-RNA complex
Function / homology
Function and homology information


intronic box C/D snoRNA processing / ribonuclease MRP activity / ribonuclease MRP complex / nucleolar ribonuclease P complex / ribonuclease P RNA binding / ribonuclease P complex / nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay / rRNA primary transcript binding / ribonuclease P / telomerase holoenzyme complex ...intronic box C/D snoRNA processing / ribonuclease MRP activity / ribonuclease MRP complex / nucleolar ribonuclease P complex / ribonuclease P RNA binding / ribonuclease P complex / nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay / rRNA primary transcript binding / ribonuclease P / 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 / metal ion binding / nucleus / cytosol / cytoplasm
Ribonuclease P/MRP protein subunit Pop5 / Pop1, N-terminal / Ribonuclease P/MRP, subunit p29 superfamily / Ribonuclease P/MRP, subunit p29 / RNase P subunit p30 / Ribonuclease P/MRP protein subunit / DNA/RNA-binding protein Alba-like / RNAse P, Rpr2/Rpp21 subunit / POPLD domain / Alba-like domain superfamily ...Ribonuclease P/MRP protein subunit Pop5 / Pop1, N-terminal / Ribonuclease P/MRP, subunit p29 superfamily / Ribonuclease P/MRP, subunit p29 / RNase P subunit p30 / Ribonuclease P/MRP protein subunit / DNA/RNA-binding protein Alba-like / RNAse P, Rpr2/Rpp21 subunit / POPLD domain / Alba-like domain superfamily / RNase P, subunit Pop3 / Ribonucleases P/MRP protein subunit Rpp20 / Polymerase/histidinol phosphatase-like / Ribonuclease P/MRP, p29 subunit / Ribonuclease P/MRP, subunit POP7 / Ribonucleases P/MRP protein subunit Pop8 / Rnp2-like domain superfamily / Rof/RNase P-like / RNAse P Rpr2/Rpp21/SNM1 subunit domain / Ribonucleases P/MRP protein subunit Pop1 / Ribonucleases P/MRP protein subunit POP1 / POPLD (NUC188) domain / RNase P subunit Pop3 / Domain of unknown function UPF0086 / Rpp14/Pop5 family / Alba / Rpp20 subunit of nuclear RNase MRP and P / RNase P subunit p30 / Alba-like domain / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Ribonucleases P/MRP protein subunit POP1 / RNases MRP/P 32.9 kDa subunit / Ribonucleases P/MRP protein subunit POP7 / Ribonuclease P protein subunit RPR2 / Ribonuclease P/MRP protein subunit RPP1 / Ribonucleases P/MRP protein subunit POP6 / Ribonucleases P/MRP protein subunit POP8 / gb:1163001456: / Ribonucleases P/MRP protein subunit POP3 / Ribonuclease P/MRP protein subunit POP5
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å
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
History
DepositionAug 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Feb 20, 2019Group: Data collection / Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.3Nov 6, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)425,18612
Polymers425,12111
Non-polymers651
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area61190 Å2
ΔGint-356 kcal/mol
Surface area160010 Å2

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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 / Details: cell / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: GenBank: 1163001456
#10: Protein Ribonuclease P protein subunit RPR2 / / RNA-processing protein RPR2 / RNase P 16.4 kDa subunit


Mass: 16375.049 Da / Num. of mol.: 1 / Details: cell / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
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 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 / Details: cell / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P41812, ribonuclease P
#3: Protein 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 / Details: cell / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53833
#6: 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 / Details: cell / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53218, ribonuclease P
#7: 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 / Details: cell / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38291, ribonuclease P
#8: 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 / Details: cell / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / 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

#5: 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 / Details: cell / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P28005, ribonuclease P
#9: 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 / Details: cell / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38786, ribonuclease P

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Protein / Non-polymers , 2 types, 2 molecules D

#11: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Protein RNases MRP/P 32.9 kDa subunit / RNA-processing protein POP4


Mass: 32933.168 Da / Num. of mol.: 1 / Details: cell / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / 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: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RNase PRibonuclease P / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Image recordingElectron dose: 50 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 / Num. of particles: 164765 / Symmetry type: POINT

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