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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


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 / ribonuclease P / rRNA primary transcript binding / ribonuclease P 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 / ribonuclease P / rRNA primary transcript binding / ribonuclease P activity / tRNA 5'-leader removal / telomerase holoenzyme complex / tRNA processing / maturation of 5.8S rRNA / rRNA processing / RNA binding / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
RNase P, subunit Pop3 / RNase P subunit Pop3 / 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 ...RNase P, subunit Pop3 / RNase P subunit Pop3 / 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 / POP1 C-terminal domain / Ribonucleases P/MRP protein subunit Rpp20/Pop7 / Rpp20 subunit of nuclear RNase MRP and P / RNase P subunit Pop5/Rpp14/Rnp2-like / RNase P subunit Pop5/Rpp14/Rnp2-like domain superfamily / Rpp14/Pop5 family / RNase P subunit p30 / Ribonuclease P subunit, Rpr2/Snm1/Rpp21 / Ribonuclease P/MRP subunit Rpp29 / 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. / Alba-like domain / Rof/RNase P-like / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily / Polymerase/histidinol phosphatase-like / Translation Initiation Factor IF3 / Metal-dependent hydrolases / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
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 P protein subunit RPR2 ...: / 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 P protein subunit RPR2 / Ribonucleases P/MRP protein subunit POP1 / Ribonucleases P/MRP protein subunit POP6 / Ribonucleases P/MRP protein subunit POP3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer'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.
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
Revision 1.4Mar 27, 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 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
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
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 / Source method: isolated from a natural source / Details: cell
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 / Source method: isolated from a natural source / Details: cell
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 / Source method: isolated from a natural source / Details: cell
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 / Source method: isolated from a natural source / Details: cell
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 / Source method: isolated from a natural source / Details: cell
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 / Source method: isolated from a natural source / Details: cell
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 / Source method: isolated from a natural source / Details: cell
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 / Source method: isolated from a natural source / Details: cell
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 / Source method: isolated from a natural source / Details: cell
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


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 / Source method: isolated from a natural source / Details: cell
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 P / Type: COMPLEX / Entity ID: #1-#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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