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- EMDB-9900: cryo-EM structure of archaeal Ribonuclease P with mature tRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-9900
Titlecryo-EM structure of archaeal Ribonuclease P with mature tRNA
Map data
Sample
  • Complex: cryo-EM structure of archaeal Ribonuclease P with mature tRNA
    • Protein or peptide: Ribonuclease P protein component 2
    • Protein or peptide: Ribonuclease P protein component 3
    • Protein or peptide: Ribonuclease P protein component 1
    • Protein or peptide: Ribonuclease P protein component 4
    • Protein or peptide: 50S ribosomal protein L7Ae
    • RNA: tRNA
    • RNA: RPR
  • Ligand: ZINC ION
KeywordsRibonuclease P / RNA-protein complex / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / ribonuclease P / box C/D sno(s)RNA binding / box C/D methylation guide snoRNP complex / ribonuclease P activity / box C/D snoRNP assembly / tRNA 5'-leader removal / ribosome biogenesis ...ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / ribonuclease P / box C/D sno(s)RNA binding / box C/D methylation guide snoRNP complex / ribonuclease P activity / box C/D snoRNP assembly / tRNA 5'-leader removal / ribosome biogenesis / rRNA binding / ribosome / structural constituent of ribosome / translation / zinc ion binding / cytoplasm
Similarity search - Function
Ribonuclease P protein subunit Rnp2, archaea / Ribonuclease P subunit RNP4 / Ribonuclease P, protein component 3, archaeal / Ribonuclease P protein subunit RNP1 / 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 ...Ribonuclease P protein subunit Rnp2, archaea / Ribonuclease P subunit RNP4 / Ribonuclease P, protein component 3, archaeal / Ribonuclease P protein subunit RNP1 / 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. / Rof/RNase P-like / Polymerase/histidinol phosphatase-like / Ribosomal protein L7Ae, archaea / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like
Similarity search - Domain/homology
Large ribosomal subunit protein eL8 / Ribonuclease P protein component 1 / Ribonuclease P protein component 2 / Ribonuclease P protein component 4 / Ribonuclease P protein component 3
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea) / Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsWan F / Lan P
CitationJournal: Nat Commun / Year: 2019
Title: Cryo-electron microscopy structure of an archaeal ribonuclease P holoenzyme.
Authors: Futang Wan / Qianmin Wang / Jing Tan / Ming Tan / Juan Chen / Shaohua Shi / Pengfei Lan / Jian Wu / Ming Lei /
Abstract: Ribonuclease P (RNase P) is an essential ribozyme responsible for tRNA 5' maturation. Here we report the cryo-EM structures of Methanocaldococcus jannaschii (Mja) RNase P holoenzyme alone and in ...Ribonuclease P (RNase P) is an essential ribozyme responsible for tRNA 5' maturation. Here we report the cryo-EM structures of Methanocaldococcus jannaschii (Mja) RNase P holoenzyme alone and in complex with a tRNA substrate at resolutions of 4.6 Å and 4.3 Å, respectively. The structures reveal that the subunits of MjaRNase P are strung together to organize the holoenzyme in a dimeric conformation required for efficient catalysis. The structures also show that archaeal RNase P is a functional chimera of bacterial and eukaryal RNase Ps that possesses bacterial-like two RNA-based anchors and a eukaryal-like protein-aided stabilization mechanism. The 3'-RCCA sequence of tRNA, which is a key recognition element for bacterial RNase P, is dispensable for tRNA recognition by MjaRNase P. The overall organization of MjaRNase P, particularly within the active site, is similar to those of bacterial and eukaryal RNase Ps, suggesting a universal catalytic mechanism for all RNase Ps.
History
DepositionMay 5, 2019-
Header (metadata) releaseJun 19, 2019-
Map releaseJun 19, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6k0b
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9900.png

Downloads & links

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Map

FileDownload / File: emd_9900.map.gz / Format: CCP4 / Size: 83.7 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 280 pix.
= 369.6 Å		1.32 Å/pix.
x 280 pix.
= 369.6 Å		1.32 Å/pix.
x 280 pix.
= 369.6 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: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.08432491 - 0.17919031
Average (Standard dev.)0.00044191844 (±0.00508289)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 369.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z369.600369.600369.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ858858858
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0840.1790.000

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Supplemental data

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Sample components

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Entire : cryo-EM structure of archaeal Ribonuclease P with mature tRNA

EntireName: cryo-EM structure of archaeal Ribonuclease P with mature tRNA
Components
  • Complex: cryo-EM structure of archaeal Ribonuclease P with mature tRNA
    • Protein or peptide: Ribonuclease P protein component 2
    • Protein or peptide: Ribonuclease P protein component 3
    • Protein or peptide: Ribonuclease P protein component 1
    • Protein or peptide: Ribonuclease P protein component 4
    • Protein or peptide: 50S ribosomal protein L7Ae
    • RNA: tRNA
    • RNA: RPR
  • Ligand: ZINC ION

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Supramolecule #1: cryo-EM structure of archaeal Ribonuclease P with mature tRNA

SupramoleculeName: cryo-EM structure of archaeal Ribonuclease P with mature tRNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)

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Macromolecule #1: Ribonuclease P protein component 2

MacromoleculeName: Ribonuclease P protein component 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Molecular weightTheoretical: 15.972156 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MIEMLKTLPP TLREKKRYIA FKILYDEELK EGEVVNLIRK AVLEYYGSWG TSKANPWLVY YDFPYGILRC QRDNVDYVKA SLILIREFK EKPVNIICLG VSGTIRKAKI KFLGIKKPKR WFVIRRERLK AKKQK

UniProtKB: Ribonuclease P protein component 2

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Macromolecule #2: Ribonuclease P protein component 3

MacromoleculeName: Ribonuclease P protein component 3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Molecular weightTheoretical: 27.394783 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRIDINRIEK EEDIKLLKEL KWNGFVFYQY DDEFSKDRYE EVKAIAESYK LKVYSGVKIK TESSKQLRDK VKKFRNKCHI ILIEGGVLK INRAAVELHD VDILSTPELG RKDSGIDHVL ARLASNHRVA IELNFKTLLN KDGYERARTL LFFRNNLKLA K KFDVPVVI ...String:
MRIDINRIEK EEDIKLLKEL KWNGFVFYQY DDEFSKDRYE EVKAIAESYK LKVYSGVKIK TESSKQLRDK VKKFRNKCHI ILIEGGVLK INRAAVELHD VDILSTPELG RKDSGIDHVL ARLASNHRVA IELNFKTLLN KDGYERARTL LFFRNNLKLA K KFDVPVVI STDAENKYQI KNPYDLRAFL NTLVEPLYAK KIMETAYKIC DFRDYLMRDN VVRYGVEIIK EEKE

UniProtKB: Ribonuclease P protein component 3

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Macromolecule #3: Ribonuclease P protein component 1

MacromoleculeName: Ribonuclease P protein component 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Molecular weightTheoretical: 10.910179 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MITPHNILRH ELIGLKVEIV EAKNKAMIGI KGKVVDETRN TLVIEKEDGR EVVIPKDIAV FLFQLKGCKV KVDGRLLIGR PEERLKKKI KILYPY

UniProtKB: Ribonuclease P protein component 1

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Macromolecule #4: Ribonuclease P protein component 4

MacromoleculeName: Ribonuclease P protein component 4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Molecular weightTheoretical: 15.610048 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MKKFLEKKLK KIAYERIDIL MSLAEEEAKK GNWDRAKRYV YLARRIAMKM RIRFPKKWKR RICKKCGTFL LYGRNARVRI KSKRYPHVV ITCLECGAIY RIPMIREKKE KRRKKLEERL KAKSNSQTS

UniProtKB: Ribonuclease P protein component 4

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Macromolecule #5: 50S ribosomal protein L7Ae

MacromoleculeName: 50S ribosomal protein L7Ae / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Molecular weightTheoretical: 12.703843 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAVYVKFKVP EEIQKELLDA VAKAQKIKKG ANEVTKAVER GIAKLVIIAE DVKPEEVVAH LPYLCEEKGI PYAYVASKQD LGKAAGLEV AASSVAIINE GDAEELKVLI EKVNVLKQ

UniProtKB: Large ribosomal subunit protein eL8

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Macromolecule #6: tRNA

MacromoleculeName: tRNA / type: rna / ID: 6 / Number of copies: 2
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 26.613838 KDa
SequenceString:
GGUGGGGUUC CCGAGCGGCC AAAGGGAGCA GACUCUAAAU CUGCCGUCAU CGACUUCGAA GGUUCGAAUC CUUCCCCCAC CAC

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Macromolecule #7: RPR

MacromoleculeName: RPR / type: rna / ID: 7 / Number of copies: 2
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)
Molecular weightTheoretical: 83.581586 KDa
SequenceString: GGAGGGGGCU GGUGACUUUC CCCUCUUUAA GAGGGGAGGA AGUUCCGCCC ACCCCAUUUA UGGGCAGCGU CCCCUGAGAA GGGGCGGGA GAUGCAGCAG AAACGACACG GCUCCGGAAG AGAUGACGAU GAUAGUGAAA GUUGAGGACU UCCGGAGAAC C GGUGAAAC ...String:
GGAGGGGGCU GGUGACUUUC CCCUCUUUAA GAGGGGAGGA AGUUCCGCCC ACCCCAUUUA UGGGCAGCGU CCCCUGAGAA GGGGCGGGA GAUGCAGCAG AAACGACACG GCUCCGGAAG AGAUGACGAU GAUAGUGAAA GUUGAGGACU UCCGGAGAAC C GGUGAAAC GGGCAUCUCC CCUGCCCGGG GUGCAAGCCG GUUUCGGCGC UUAGCCGAAU GUCACCGAAA UUACAGAAGG CG GGCUAUA GCCCCCAUUU U

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 2 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.32 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 150000
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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