+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9900 | |||||||||
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Title | cryo-EM structure of archaeal Ribonuclease P with mature tRNA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Ribonuclease 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 / tRNA 5'-leader removal / box C/D snoRNP assembly / 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 / tRNA 5'-leader removal / box C/D snoRNP assembly / ribosome biogenesis / rRNA binding / ribosome / structural constituent of ribosome / translation / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Methanocaldococcus jannaschii (archaea) / Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
Authors | Wan F / Lan P | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9900.map.gz | 6.6 MB | EMDB map data format | |
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Header (meta data) | emd-9900-v30.xml emd-9900.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
Images | emd_9900.png | 150.6 KB | ||
Filedesc metadata | emd-9900.cif.gz | 5.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9900 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9900 | HTTPS FTP |
-Related structure data
Related structure data | 6k0bMC 6k0aC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9900.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : cryo-EM structure of archaeal Ribonuclease P with mature tRNA
Entire | Name: cryo-EM structure of archaeal Ribonuclease P with mature tRNA |
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Components |
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-Supramolecule #1: cryo-EM structure of archaeal Ribonuclease P with mature tRNA
Supramolecule | Name: cryo-EM structure of archaeal Ribonuclease P with mature tRNA type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
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Source (natural) | Organism: Methanocaldococcus jannaschii (archaea) |
-Macromolecule #1: Ribonuclease P protein component 2
Macromolecule | Name: Ribonuclease P protein component 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribonuclease P |
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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 weight | Theoretical: 15.972156 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MIEMLKTLPP TLREKKRYIA FKILYDEELK EGEVVNLIRK AVLEYYGSWG TSKANPWLVY YDFPYGILRC QRDNVDYVKA SLILIREFK EKPVNIICLG VSGTIRKAKI KFLGIKKPKR WFVIRRERLK AKKQK UniProtKB: Ribonuclease P protein component 2 |
-Macromolecule #2: Ribonuclease P protein component 3
Macromolecule | Name: Ribonuclease P protein component 3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribonuclease P |
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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 weight | Theoretical: 27.394783 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 |
-Macromolecule #3: Ribonuclease P protein component 1
Macromolecule | Name: Ribonuclease P protein component 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribonuclease P |
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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 weight | Theoretical: 10.910179 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MITPHNILRH ELIGLKVEIV EAKNKAMIGI KGKVVDETRN TLVIEKEDGR EVVIPKDIAV FLFQLKGCKV KVDGRLLIGR PEERLKKKI KILYPY UniProtKB: Ribonuclease P protein component 1 |
-Macromolecule #4: Ribonuclease P protein component 4
Macromolecule | Name: Ribonuclease P protein component 4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribonuclease P |
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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 weight | Theoretical: 15.610048 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MKKFLEKKLK KIAYERIDIL MSLAEEEAKK GNWDRAKRYV YLARRIAMKM RIRFPKKWKR RICKKCGTFL LYGRNARVRI KSKRYPHVV ITCLECGAIY RIPMIREKKE KRRKKLEERL KAKSNSQTS UniProtKB: Ribonuclease P protein component 4 |
-Macromolecule #5: 50S ribosomal protein L7Ae
Macromolecule | Name: 50S ribosomal protein L7Ae / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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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 weight | Theoretical: 12.703843 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MAVYVKFKVP EEIQKELLDA VAKAQKIKKG ANEVTKAVER GIAKLVIIAE DVKPEEVVAH LPYLCEEKGI PYAYVASKQD LGKAAGLEV AASSVAIINE GDAEELKVLI EKVNVLKQ UniProtKB: Large ribosomal subunit protein eL8 |
-Macromolecule #6: tRNA
Macromolecule | Name: tRNA / type: rna / ID: 6 / Number of copies: 2 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 26.613838 KDa |
Sequence | String: GGUGGGGUUC CCGAGCGGCC AAAGGGAGCA GACUCUAAAU CUGCCGUCAU CGACUUCGAA GGUUCGAAUC CUUCCCCCAC CAC |
-Macromolecule #7: RPR
Macromolecule | Name: RPR / type: rna / ID: 7 / Number of copies: 2 |
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Source (natural) | Organism: Methanocaldococcus jannaschii (archaea) |
Molecular weight | Theoretical: 83.581586 KDa |
Sequence | String: 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 |
-Macromolecule #8: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.32 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP |
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Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |
Final reconstruction | Applied 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 |