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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12878 | |||||||||
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Title | RNA-free Ribonuclease P from Halorhodospira halophila | |||||||||
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![]() | RNAseP / metallonuclease / HARP / HYDROLASE | |||||||||
Function / homology | RNA-free ribonuclease P / PINc domain ribonuclease / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / PIN-like domain superfamily / RNA-free ribonuclease P![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.37 Å | |||||||||
![]() | Altegoer F / Bange G | |||||||||
![]() | ![]() Title: Structure and mechanistic features of the prokaryotic minimal RNase P. Authors: Rebecca Feyh / Nadine B Waeber / Simone Prinz / Pietro Ivan Giammarinaro / Gert Bange / Georg Hochberg / Roland K Hartmann / Florian Altegoer / ![]() Abstract: Endonucleolytic removal of 5'-leader sequences from tRNA precursor transcripts (pre-tRNAs) by ribonuclease P (RNase P) is essential for protein synthesis. Beyond RNA-based RNase P enzymes, protein- ...Endonucleolytic removal of 5'-leader sequences from tRNA precursor transcripts (pre-tRNAs) by ribonuclease P (RNase P) is essential for protein synthesis. Beyond RNA-based RNase P enzymes, protein-only versions of the enzyme exert this function in various eukarya (there termed PRORPs) and in some bacteria ( and close relatives); both enzyme types belong to distinct subgroups of the PIN domain metallonuclease superfamily. Homologs of RNase P (HARPs) are also expressed in some other bacteria and many archaea, where they coexist with RNA-based RNase P and do not represent the main RNase P activity. Here, we solved the structure of the bacterial HARP from by cryo-electron microscopy, revealing a novel screw-like dodecameric assembly. Biochemical experiments demonstrate that oligomerization is required for RNase P activity of HARPs. We propose that the tRNA substrate binds to an extended spike-helix (SH) domain that protrudes from the screw-like assembly to position the 5'-end in close proximity to the active site of the neighboring dimer. The structure suggests that eukaryotic PRORPs and prokaryotic HARPs recognize the same structural elements of pre-tRNAs (tRNA elbow region and cleavage site). Our analysis thus delivers the structural and mechanistic basis for pre-tRNA processing by the prokaryotic HARP system. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 33 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.3 KB 11.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.9 KB | Display | ![]() |
Images | ![]() | 119.9 KB | ||
Filedesc metadata | ![]() | 5.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 560.3 KB | Display | ![]() |
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Full document | ![]() | 559.8 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7og5MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.833 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Dodecameric assembly of minimal RNAseP system from Halorhodospira...
Entire | Name: Dodecameric assembly of minimal RNAseP system from Halorhodospira halophila |
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Components |
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-Supramolecule #1: Dodecameric assembly of minimal RNAseP system from Halorhodospira...
Supramolecule | Name: Dodecameric assembly of minimal RNAseP system from Halorhodospira halophila type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 390 KDa |
-Macromolecule #1: RNA-free ribonuclease P
Macromolecule | Name: RNA-free ribonuclease P / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: ribonuclease P |
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Source (natural) | Organism: ![]() Strain: DSM 244 / SL1 |
Molecular weight | Theoretical: 24.051338 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSHMASRRFV LDTSVFTNPD VYLRFDEEPM QAISVFLGLA RRADAEFYMP GPVYQELCNL RSMDLIGAEF ETEVYIRSPR RFSMTIPSE VLYEFIEEVR TRIQRGLRIA EEHARQAGQA ESLPPELITQ LRERYREAMR RGILDSREDI DVVLLAYELD A TLVSADEG ...String: GSHMASRRFV LDTSVFTNPD VYLRFDEEPM QAISVFLGLA RRADAEFYMP GPVYQELCNL RSMDLIGAEF ETEVYIRSPR RFSMTIPSE VLYEFIEEVR TRIQRGLRIA EEHARQAGQA ESLPPELITQ LRERYREAMR RGILDSREDI DVVLLAYELD A TLVSADEG MRKFAERIGI KLVNPRYLRG VMQNLAGDDP GHAPPCGPDQ PAG UniProtKB: RNA-free ribonuclease P |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 8 mg/mL | |||||||||
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Buffer | pH: 8 Component:
Details: Solutions were prepared freshly and filtered through a 0.2 um filter | |||||||||
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 11s with blot force -1 before plunging. | |||||||||
Details | The sample was monodisperse |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 8393 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 181 |
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Output model | ![]() PDB-7og5: |