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- EMDB-9622: Cryo-EM structure of yeast Ribonuclease P with pre-tRNA substrate -

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Basic information

Entry
Database: EMDB / ID: 9622
TitleCryo-EM structure of yeast Ribonuclease P with pre-tRNA substrate
Map data
SampleRNase P with pre-tRNA substrate
  • RNase PRibonuclease P
  • pre-tRNA
  • (nucleic-acidNucleic acid) x 2
  • (Ribonucleases P/MRP protein subunit ...) x 5
  • RNases MRP/P 32.9 kDa subunit
  • (Ribonuclease P/MRP protein subunit ...) x 2
  • Ribonuclease P protein subunit RPR2
  • (ligand) x 2
Function / homologyRNase P, subunit Pop3 / Ribonuclease P/MRP, subunit POP7 / Ribonuclease P/MRP, p29 subunit / Ribonuclease P/MRP protein subunit Pop5 / Polymerase/histidinol phosphatase-like / Ribonucleases P/MRP protein subunit Rpp20 / POPLD domain / Pop1, N-terminal / RNAse P, Rpr2/Rpp21 subunit / DNA/RNA-binding protein Alba-like ...RNase P, subunit Pop3 / Ribonuclease P/MRP, subunit POP7 / Ribonuclease P/MRP, p29 subunit / Ribonuclease P/MRP protein subunit Pop5 / Polymerase/histidinol phosphatase-like / Ribonucleases P/MRP protein subunit Rpp20 / 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 / Ribonucleases P/MRP protein subunit Pop8 / Rof/RNase P-like / Alba-like domain superfamily / Ribonucleases P/MRP protein subunit Pop6 / 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 / Rpp20 subunit of nuclear RNase MRP and P / ribonuclease MRP activity / intronic box C/D snoRNA processing / ribonuclease MRP complex / nucleolar ribonuclease P complex / ribonuclease P RNA binding / ribonuclease P complex / nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay / ribonuclease P / rRNA primary transcript binding / 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
Function and homology information
SourceSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (baker's yeast) / Saccharomyces cerevisiae S288c (yeast)
Methodsingle 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 ReportPDB-ID: 6ah3

SummaryFull reportAbout validation report
DateDeposition: Aug 16, 2018 / Header (metadata) release: Oct 17, 2018 / Map release: Oct 17, 2018 / Last update: Oct 17, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6ah3
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9622.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.32 Å/pix.
= 337.92 Å
256 pix
1.32 Å/pix.
= 337.92 Å
256 pix
1.32 Å/pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour Level:0.025 (by author), 0.04 (movie #1):
Minimum - Maximum-0.1938393 - 0.30816835
Average (Standard dev.)0.00026609402 (0.0092275115)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.00.00.0
Limit255.0255.0255.0
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z337.920337.920337.920
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1940.3080.000

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Supplemental data

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Sample components

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Entire RNase P with pre-tRNA substrate

EntireName: RNase P with pre-tRNA substrate / Number of components: 16

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Component #1: protein, RNase P with pre-tRNA substrate

ProteinName: RNase P with pre-tRNA substrate / Recombinant expression: No

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Component #2: protein, RNase P

ProteinName: RNase PRibonuclease P / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #3: protein, pre-tRNA

ProteinName: pre-tRNA / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast) / Vector: pGlms

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Component #4: nucleic-acid, Ribonuclease P RNA

Nucleic-acidName: Ribonuclease P RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUGGAACAGU GGUAAUUCCU ACGAUUAAGA AACCUGUUUA CAGAAGGAUC CCCACCUAUG GGCGGGUUAU CAGAUAUUAU CAGGUGGGAA AUUCGGUGGA ACACAGUGGA GCCUUGUCCU CCGGGUUAAU GUCGCUUUUG GCAUUGGCCC CUGCUCCUGA GAGAAGAAAU AUACUGGGGA ACCAGUCUUU ACCGACCGUU GUUAUCAGAA AUUCACGGAG UUCGGCCUAG GUCGGACUCC GAUGGGAACG GCAACGGUUG UUCCGUUUGA CUUGUCGCCC GCUACGGCGU GAGCGUCAAG GUCUGUUGAG UGCAAUCGUA GGACGUCAUU AGUGGCGAAC CCGAUACCGA UUACUGCUGC UGUUCCAGC
MassTheoretical: 118.857781 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #5: protein, Ribonucleases P/MRP protein subunit POP1

ProteinName: Ribonucleases P/MRP protein subunit POP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 100.559555 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #6: protein, Ribonucleases P/MRP protein subunit POP3

ProteinName: Ribonucleases P/MRP protein subunit POP3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.643721 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #7: protein, RNases MRP/P 32.9 kDa subunit

ProteinName: RNases MRP/P 32.9 kDa subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.933168 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #8: protein, Ribonuclease P/MRP protein subunit POP5

ProteinName: Ribonuclease P/MRP protein subunit POP5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.60159 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #9: protein, Ribonucleases P/MRP protein subunit POP6

ProteinName: Ribonucleases P/MRP protein subunit POP6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.234959 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #10: protein, Ribonucleases P/MRP protein subunit POP7

ProteinName: Ribonucleases P/MRP protein subunit POP7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.844284 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #11: protein, Ribonucleases P/MRP protein subunit POP8

ProteinName: Ribonucleases P/MRP protein subunit POP8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.530351 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #12: protein, Ribonuclease P/MRP protein subunit RPP1

ProteinName: Ribonuclease P/MRP protein subunit RPP1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 32.270262 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #13: protein, Ribonuclease P protein subunit RPR2

ProteinName: Ribonuclease P protein subunit RPR2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.375049 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #14: nucleic-acid, pre-tRNA

Nucleic-acidName: pre-tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AGAAGCGGAU UUAGCUCAGU UGGGAGAGCG CCAGACUGAA GAUCUGGAGG UCCUGUGUUC GAUCCACAGA AUUCGCAUUU
MassTheoretical: 25.830324 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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Component #15: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #16: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.5625 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 176896
3D reconstructionResolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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