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- EMDB-21564: Structure of yeast RNase MRP holoenzyme -

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Basic information

Entry
Database: EMDB / ID: EMD-21564
TitleStructure of yeast RNase MRP holoenzyme
Map dataRNase MRP holoenzyme
Sample
  • Complex: Ribonuclease MRP
    • RNA: RNA component of RNase MRP NME1
    • Protein or peptide: Ribonucleases P/MRP protein subunit POP1
    • 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 MRP protein subunit SNM1
    • Protein or peptide: Ribonuclease MRP protein subunit RMP1
Keywordsribozyme / RNP / ribonucleoprotein / HYDROLASE
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 / plasmid partitioning / ribonuclease P / nuclease 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 / plasmid partitioning / ribonuclease P / nuclease activity / rRNA primary transcript binding / ribonuclease P activity / telomerase holoenzyme complex / tRNA 5'-leader removal / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / tRNA processing / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA processing / rRNA processing / nucleolus / RNA binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / Ribonuclease MRP protein subunit RMP1 / 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 ...: / : / Ribonuclease MRP protein subunit RMP1 / 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 MRP protein subunit SNM1 / Ribonucleases P/MRP protein subunit POP1 / Ribonucleases P/MRP protein subunit POP6 / Ribonuclease MRP protein subunit RMP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsPerederina A / Li D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM135598 United States
CitationJournal: Nat Commun / Year: 2020
Title: Cryo-EM structure of catalytic ribonucleoprotein complex RNase MRP.
Authors: Anna Perederina / Di Li / Hyunwook Lee / Carol Bator / Igor Berezin / Susan L Hafenstein / Andrey S Krasilnikov /
Abstract: RNase MRP is an essential eukaryotic ribonucleoprotein complex involved in the maturation of rRNA and the regulation of the cell cycle. RNase MRP is related to the ribozyme-based RNase P, but it has ...RNase MRP is an essential eukaryotic ribonucleoprotein complex involved in the maturation of rRNA and the regulation of the cell cycle. RNase MRP is related to the ribozyme-based RNase P, but it has evolved to have distinct cellular roles. We report a cryo-EM structure of the S. cerevisiae RNase MRP holoenzyme solved to 3.0 Å. We describe the structure of this 450 kDa complex, interactions between its components, and the organization of its catalytic RNA. We show that some of the RNase MRP proteins shared with RNase P undergo an unexpected RNA-driven remodeling that allows them to bind to divergent RNAs. Further, we reveal how this RNA-driven protein remodeling, acting together with the introduction of new auxiliary elements, results in the functional diversification of RNase MRP and its progenitor, RNase P, and demonstrate structural underpinnings of the acquisition of new functions by catalytic RNPs.
History
DepositionMar 17, 2020-
Header (metadata) releaseJul 15, 2020-
Map releaseJul 15, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6w6v
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21564.png

Downloads & links

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Map

FileDownload / File: emd_21564.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRNase MRP holoenzyme
Voxel sizeX=Y=Z: 0.665 Å
Density
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.4
Minimum - Maximum-1.5965668 - 3.1305418
Average (Standard dev.)-0.00000000000434 (±0.09417193)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 340.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6650.6650.665
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z340.480340.480340.480
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S312
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-1.5973.131-0.000

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Supplemental data

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Sample components

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Entire : Ribonuclease MRP

EntireName: Ribonuclease MRP
Components
  • Complex: Ribonuclease MRP
    • RNA: RNA component of RNase MRP NME1
    • Protein or peptide: Ribonucleases P/MRP protein subunit POP1
    • 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 MRP protein subunit SNM1
    • Protein or peptide: Ribonuclease MRP protein subunit RMP1

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Supramolecule #1: Ribonuclease MRP

SupramoleculeName: Ribonuclease MRP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 450 KDa

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Macromolecule #1: RNA component of RNase MRP NME1

MacromoleculeName: RNA component of RNase MRP NME1 / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 108.767664 KDa
SequenceString: AAUCCAUGAC CAAAGAAUCG UCACAAAUCG AAGCUUACAA AAUGGAGUAA AAUUUUUUUU ACUCAGUAAU AUGCUUUGGG UUGAAAGUC UCCCACCAAU UCGUAUGCGG AAAACGUAAU GAGAUUUAAA AAUUUUAAAU UGUUUAAAUC AACUCAUUAA G GAGGAUGC ...String:
AAUCCAUGAC CAAAGAAUCG UCACAAAUCG AAGCUUACAA AAUGGAGUAA AAUUUUUUUU ACUCAGUAAU AUGCUUUGGG UUGAAAGUC UCCCACCAAU UCGUAUGCGG AAAACGUAAU GAGAUUUAAA AAUUUUAAAU UGUUUAAAUC AACUCAUUAA G GAGGAUGC CCUUGGGUAU UCUGCUUCUU GACCUGGUAC CUCUAUUGCA GGGUACUGGU GUUUUCUUCG GUACUGGAUU CC GUUUGUA UGGAAUCUAA ACCAUAGUUA UGACGAUUGC UCUUUCCCGU GCUGGAUCGA GUAACCCAAU GGAGCUUACU AUU CUUGGU CCAUGGAUUC ACCC

GENBANK: GENBANK: Z14231.1

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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: Saccharomyces cerevisiae S288C (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

UniProtKB: Ribonucleases P/MRP protein subunit POP1

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Macromolecule #3: RNases MRP/P 32.9 kDa subunit

MacromoleculeName: RNases MRP/P 32.9 kDa subunit / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (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

UniProtKB: RNases MRP/P 32.9 kDa subunit

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Macromolecule #4: Ribonuclease P/MRP protein subunit POP5

MacromoleculeName: Ribonuclease P/MRP protein subunit POP5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Saccharomyces cerevisiae S288C (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

UniProtKB: Ribonuclease P/MRP protein subunit POP5

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Macromolecule #5: Ribonucleases P/MRP protein subunit POP6

MacromoleculeName: Ribonucleases P/MRP protein subunit POP6 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Saccharomyces cerevisiae S288C (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

UniProtKB: Ribonucleases P/MRP protein subunit POP6

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Macromolecule #6: Ribonucleases P/MRP protein subunit POP7

MacromoleculeName: Ribonucleases P/MRP protein subunit POP7 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Saccharomyces cerevisiae S288C (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

UniProtKB: Ribonucleases P/MRP protein subunit POP7

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Macromolecule #7: Ribonucleases P/MRP protein subunit POP8

MacromoleculeName: Ribonucleases P/MRP protein subunit POP8 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Saccharomyces cerevisiae S288C (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

UniProtKB: Ribonucleases P/MRP protein subunit POP8

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Macromolecule #8: Ribonuclease P/MRP protein subunit RPP1

MacromoleculeName: Ribonuclease P/MRP protein subunit RPP1 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Saccharomyces cerevisiae S288C (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

UniProtKB: Ribonuclease P/MRP protein subunit RPP1

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Macromolecule #9: Ribonuclease MRP protein subunit SNM1

MacromoleculeName: Ribonuclease MRP protein subunit SNM1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 22.578955 KDa
SequenceString: MNKDQAEKYQ ERSLRQKYNL LHVLPTLNSR ALSGLYYKNF HNSVKRYQIM LPEQLKSGKF CSHCGCVYVP NFNASLQLTT NTEQGDSDE LGGESMEGPK KCIQVNCLNC EKSKLFEWKS EFVVPTFGQD VSPMINSTSS GKVSYAVKKP QKSKTSTGKE R SKKRKLNS ...String:
MNKDQAEKYQ ERSLRQKYNL LHVLPTLNSR ALSGLYYKNF HNSVKRYQIM LPEQLKSGKF CSHCGCVYVP NFNASLQLTT NTEQGDSDE LGGESMEGPK KCIQVNCLNC EKSKLFEWKS EFVVPTFGQD VSPMINSTSS GKVSYAVKKP QKSKTSTGKE R SKKRKLNS LTNLLSKRNQ EKKMEKKKSS SLSLESFMKS

UniProtKB: Ribonuclease MRP protein subunit SNM1

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Macromolecule #10: Ribonuclease MRP protein subunit RMP1

MacromoleculeName: Ribonuclease MRP protein subunit RMP1 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 23.657668 KDa
SequenceString: MDEMDNVIRS LEQEYRLILL LNHRNKNQHR AASWYGSFNE MKRNCGQIIT LFSSRRLQAK RLKDVEWVKL HRLLQRALFR QLKRWYWQF NGVIALGQFV TLGCTLVTLL ANVRALYMRL WEINETEFIR CGCLIKNLPR TKAKSVVNDV EELGEIIDED I GNNVQENE ...String:
MDEMDNVIRS LEQEYRLILL LNHRNKNQHR AASWYGSFNE MKRNCGQIIT LFSSRRLQAK RLKDVEWVKL HRLLQRALFR QLKRWYWQF NGVIALGQFV TLGCTLVTLL ANVRALYMRL WEINETEFIR CGCLIKNLPR TKAKSVVNDV EELGEIIDED I GNNVQENE LVITSIPKPL TENCKKKKKR KKKNKSAIDG IFG

UniProtKB: Ribonuclease MRP protein subunit RMP1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 8
GridPretreatment - Type: GLOW DISCHARGE / Details: unspecified
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: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 39.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 155205

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