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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: EMD-9622
TitleCryo-EM structure of yeast Ribonuclease P with pre-tRNA substrate
Map data
Sample
  • Complex: RNase P with pre-tRNA substrate
    • Complex: RNase PRibonuclease P
      • RNA: x 1 types
      • Protein or peptide: x 9 types
    • Complex: pre-tRNA
      • RNA: x 1 types
  • Ligand: x 2 types
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 / telomerase holoenzyme complex ...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 / telomerase holoenzyme complex / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / rRNA processing / RNA binding / metal ion binding / nucleus / cytosol / cytoplasm
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 / 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
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 (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (brewer's yeast) / Saccharomyces cerevisiae S288c (yeast)
Methodsingle 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 16, 2018-
Header (metadata) releaseOct 17, 2018-
Map releaseOct 17, 2018-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBj / Status: Released

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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

emd_9622.png

Downloads & links

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Map

FileDownload / File: emd_9622.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.04
Minimum - Maximum-0.1938393 - 0.30816835
Average (Standard dev.)0.00026609402 (±0.0092275115)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

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
Components
  • Complex: RNase P with pre-tRNA substrate
    • Complex: RNase PRibonuclease P
      • RNA: Ribonuclease P RNA
      • Protein or peptide: Ribonucleases P/MRP protein subunit POP1
      • Protein or peptide: Ribonucleases P/MRP protein subunit POP3
      • Protein or peptide: RNases MRP/P 32.9 kDa subunit
      • Protein or peptide: Ribonuclease P/MRP protein subunit POP5
      • Protein or peptide: Ribonucleases P/MRP protein subunit POP6
      • Protein or peptide: Ribonucleases P/MRP protein subunit POP7
      • Protein or peptide: Ribonucleases P/MRP protein subunit POP8
      • Protein or peptide: Ribonuclease P/MRP protein subunit RPP1
      • Protein or peptide: Ribonuclease P protein subunit RPR2
    • Complex: pre-tRNA
      • RNA: pre-tRNA
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: RNase P with pre-tRNA substrate

SupramoleculeName: RNase P with pre-tRNA substrate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11

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Supramolecule #2: RNase P

SupramoleculeName: RNase P / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#10
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Supramolecule #3: pre-tRNA

SupramoleculeName: pre-tRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #11
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant plasmid: pGlms

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Macromolecule #1: Ribonuclease P RNA

MacromoleculeName: Ribonuclease P RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 118.857781 KDa
SequenceString: GUGGAACAGU GGUAAUUCCU ACGAUUAAGA AACCUGUUUA CAGAAGGAUC CCCACCUAUG GGCGGGUUAU CAGAUAUUAU CAGGUGGGA AAUUCGGUGG AACACAGUGG AGCCUUGUCC UCCGGGUUAA UGUCGCUUUU GGCAUUGGCC CCUGCUCCUG A GAGAAGAA ...String:
GUGGAACAGU GGUAAUUCCU ACGAUUAAGA AACCUGUUUA CAGAAGGAUC CCCACCUAUG GGCGGGUUAU CAGAUAUUAU CAGGUGGGA AAUUCGGUGG AACACAGUGG AGCCUUGUCC UCCGGGUUAA UGUCGCUUUU GGCAUUGGCC CCUGCUCCUG A GAGAAGAA AUAUACUGGG GAACCAGUCU UUACCGACCG UUGUUAUCAG AAAUUCACGG AGUUCGGCCU AGGUCGGACU CC GAUGGGA ACGGCAACGG UUGUUCCGUU UGACUUGUCG CCCGCUACGG CGUGAGCGUC AAGGUCUGUU GAGUGCAAUC GUA GGACGU CAUUAGUGGC GAACCCGAUA CCGAUUACUG CUGCUGUUCC AGC

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Macromolecule #11: pre-tRNA

MacromoleculeName: pre-tRNA / type: rna / ID: 11 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Molecular weightTheoretical: 25.830324 KDa
SequenceString:
AGAAGCGGAU UUAGCUCAGU UGGGAGAGCG CCAGACUGAA GAUCUGGAGG UCCUGUGUUC GAUCCACAGA AUUCGCAUUU

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Macromolecule #2: Ribonucleases P/MRP protein subunit POP1

MacromoleculeName: Ribonucleases P/MRP protein subunit POP1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 100.559555 KDa
SequenceString: MSGSLSRGNG GKKVLNKNQL LKRNRIRNAR SIRAEAVAAS STKTGTPSDL SESGSKLNVD QFISSRQFEV KQLQLAMHNS KAASSTRIF QALPRKLRRR TASHNVRRIP KRMRNRALRE MRKSDQQDVL KGSSASSRKA HGLNAKQLYK ARMSIKLLRL A SKSTSMKL ...String:
MSGSLSRGNG GKKVLNKNQL LKRNRIRNAR SIRAEAVAAS STKTGTPSDL SESGSKLNVD QFISSRQFEV KQLQLAMHNS KAASSTRIF QALPRKLRRR TASHNVRRIP KRMRNRALRE MRKSDQQDVL KGSSASSRKA HGLNAKQLYK ARMSIKLLRL A SKSTSMKL SMPPEVTSSN CHVRQKIKTL KRMIKESSTA NPNIKLLNNR MGSYDCTGVN ELAPIPKGRV KYTKRQKHFA WL PTHIWNA KRSHMMKRWG YQMVWAPTQK CFKLTHRLGG DTCSSDGALC MDSSYIGTII VKDKSNDSEG DFLKSIIGKL TAE RANLRK YREGQVLFQG LIYSFNEENG EDSTKPLGPC DVFWVQKDTA IIRLHPSIYT QVFNILLQHK EKLTVQDCRY SLAS VTLKG AKALESLASC LRSTEYSKSF EQFKMVSMIT DHNALPQRCT FAFEAIDPRH LAAPKKLNDS QRKTVNSDDI LSLHE NYPQ DEINAVFNEL CDPESRTQSY NNQNTLKEIS ARRYKLLTAT PNSINKTTVP FKESDDPSIP LVIIRRLKTR DWIVVL PWF WLLPLWHLLN RIPRMYHIGL RQFQQIQYEN KQLYFPDDYP FTQLGYIENS FYKKEASKTK WDRKPMGKRI NFEKIKD IH NTKLPAYSGE IGDFFSSDWR FLQILRNGID YLQRNDKTLE LMDSKKTGQF NAQGVRDINC VNDVLEFCKD YEAKTKAM S LSIEENIPVA LCKNRKCQFR TPDSISVNSS SFSLTFFPRC IIAVSCTLLE RGHPKDNARI YQVPEKDLEH WLQLAKGVY RPNGRKDHDL KIPLPEVHDL IGFITSGTYH LNCGNGMGIG FIDHHAAIRQ PTRYVLIRNV GTNTYRLGEW SKISV

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Macromolecule #3: Ribonucleases P/MRP protein subunit POP3

MacromoleculeName: Ribonucleases P/MRP protein subunit POP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 22.643721 KDa
SequenceString: MSGSLKSLDK KIAKRRQVYK PVLDNPFTNE AHMWPRVHDQ PLIWQLLQSS IINKLIHIQS KENYPWELYT DFNEIVQYLS GAHGNSDPV CLFVCNKDPD VPLVLLQQIP LLCYMAPMTV KLVQLPKSAM DTFKSVSKYG MLLLRCDDRV DKKFVSQIQK N VDLLQFPW ...String:
MSGSLKSLDK KIAKRRQVYK PVLDNPFTNE AHMWPRVHDQ PLIWQLLQSS IINKLIHIQS KENYPWELYT DFNEIVQYLS GAHGNSDPV CLFVCNKDPD VPLVLLQQIP LLCYMAPMTV KLVQLPKSAM DTFKSVSKYG MLLLRCDDRV DKKFVSQIQK N VDLLQFPW LNAIKYRPTS VKLLKTTVPI VSKKRQK

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Macromolecule #4: RNases MRP/P 32.9 kDa subunit

MacromoleculeName: RNases MRP/P 32.9 kDa subunit / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 32.933168 KDa
SequenceString: MDRTQTFIKD CLFTKCLEDP EKPFNENRFQ DTLLLLPTDG GLTSRLQRQQ RKSKLNLDNL QKVSQLESAD KQLEKRDYQR INKNSKIAL REYINNCKKN TKKCLKLAYE NKITDKEDLL HYIEEKHPTI YESLPQYVDF VPMYKELWIN YIKELLNITK N LKTFNGSL ...String:
MDRTQTFIKD CLFTKCLEDP EKPFNENRFQ DTLLLLPTDG GLTSRLQRQQ RKSKLNLDNL QKVSQLESAD KQLEKRDYQR INKNSKIAL REYINNCKKN TKKCLKLAYE NKITDKEDLL HYIEEKHPTI YESLPQYVDF VPMYKELWIN YIKELLNITK N LKTFNGSL ALLKLSMADY NGALLRVTKS KNKTLIGLQG IVIWDSQKFF IMIVKGNIID EIKCIPKKGT VFQFEIPISD DD DSALRYS ILGDRFKYRS VDRAGRKFKS RRCDDMLYYI QN

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Macromolecule #5: Ribonuclease P/MRP protein subunit POP5

MacromoleculeName: Ribonuclease P/MRP protein subunit POP5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 19.60159 KDa
SequenceString:
MVRLKSRYIL FEIIFPPTDT NVEESVSKAD ILLSHHRASP ADVSIKSILQ EIRRSLSLNL GDYGSAKCNS LLQLKYFSNK TSTGIIRCH REDCDLVIMA LMLMSKIGDV DGLIVNPVKV SGTIKKIEQF AMRRNSKILN IIKCSQSSHL SDNDFIINDF K KIGRENEN ENEDD

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Macromolecule #6: Ribonucleases P/MRP protein subunit POP6

MacromoleculeName: Ribonucleases P/MRP protein subunit POP6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 18.234959 KDa
SequenceString:
MINGVYYNEI SRDLDISSST QCLRFLKETV IPSLANNGNN STSIQYHGIS KNDNIKKSVN KLDKQINMAD RSLGLQQVVC IFSYGPHIQ KMLSILEIFK KGYIKNNKKI YQWNKLTSFD IKREGRNELQ EERLKVPILV TLVSDSEIID LNLHSFTKQ

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Macromolecule #7: Ribonucleases P/MRP protein subunit POP7

MacromoleculeName: Ribonucleases P/MRP protein subunit POP7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 15.844284 KDa
SequenceString:
MALKKNTHNK STKRVTKHPS LKTLTHKQIH TTIFVKSTTP YVSALKRINK FLDSVHKQGS SYVAVLGMGK AVEKTLALGC HFQDQKNKK IEVYTKTIEV LDEVITEGQA DIDMESDVED DDKETQLKKR AVSGVELRIY V

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Macromolecule #8: Ribonucleases P/MRP protein subunit POP8

MacromoleculeName: Ribonucleases P/MRP protein subunit POP8 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 15.530351 KDa
SequenceString:
MGKKTFREWQ YFKLSITSFD QDVDDAHAID QMTWRQWLNN ALKRSYGIFG EGVEYSFLHV DDKLAYIRVN HADKDTFSSS ISTYISTDE LVGSPLTVSI LQESSSLRLL EVTDDDRLWL KKVMEEEEQD CKCI

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Macromolecule #9: Ribonuclease P/MRP protein subunit RPP1

MacromoleculeName: Ribonuclease P/MRP protein subunit RPP1 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 32.270262 KDa
SequenceString: MLVDLNVPWP QNSYADKVTS QAVNNLIKTL STLHMLGYTH IAINFTVNHS EKFPNDVKLL NPIDIKRRFG ELMDRTGLKL YSRITLIID DPSKGQSLSK ISQAFDIVAA LPISEKGLTL STTNLDIDLL TFQYGSRLPT FLKHKSICSC VNRGVKLEIV Y GYALRDVQ ...String:
MLVDLNVPWP QNSYADKVTS QAVNNLIKTL STLHMLGYTH IAINFTVNHS EKFPNDVKLL NPIDIKRRFG ELMDRTGLKL YSRITLIID DPSKGQSLSK ISQAFDIVAA LPISEKGLTL STTNLDIDLL TFQYGSRLPT FLKHKSICSC VNRGVKLEIV Y GYALRDVQ ARRQFVSNVR SVIRSSRSRG IVIGSGAMSP LECRNILGVT SLIKNLGLPS DRCSKAMGDL ASLVLLNGRL RN KSHKQTI VTGGGSGNGD DVVNDVQGID DVQTIKVVKR SMDAEQLGHA SKRHKP

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Macromolecule #10: Ribonuclease P protein subunit RPR2

MacromoleculeName: Ribonuclease P protein subunit RPR2 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Baker's yeast (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 16.375049 KDa
SequenceString:
MGKKAHGGKM KPEIDENGTL LVPPPRTIAN QDHFHRLNYL YQISAYQTRA RQKARTDAHT PLARNYIKSM DLISKKTKTS LLPTIKRTI CKKCHRLLWT PKKLEITSDG ALSVMCGCGT VKRFNIGADP NYRTYSEREG NLLNS

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Macromolecule #12: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 12 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #13: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 13 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5625 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 176896

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