+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26636 | |||||||||
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Title | E.coli RNaseP Holoenzyme with Mg2+ | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ribozyme / protein-RNA complex / divalent ion / RNA / HYDROLASE-RNA complex | |||||||||
Function / homology | Function and homology information 3'-tRNA processing endoribonuclease activity / ribonuclease P complex / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / tRNA binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Huang W / Taylor DJ | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural and mechanistic basis for recognition of alternative tRNA precursor substrates by bacterial ribonuclease P. Authors: Jiaqiang Zhu / Wei Huang / Jing Zhao / Loc Huynh / Derek J Taylor / Michael E Harris / Abstract: Binding of precursor tRNAs (ptRNAs) by bacterial ribonuclease P (RNase P) involves an encounter complex (ES) that isomerizes to a catalytic conformation (ES*). However, the structures of ...Binding of precursor tRNAs (ptRNAs) by bacterial ribonuclease P (RNase P) involves an encounter complex (ES) that isomerizes to a catalytic conformation (ES*). However, the structures of intermediates and the conformational changes that occur during binding are poorly understood. Here, we show that pairing between the 5' leader and 3'RCCA extending the acceptor stem of ptRNA inhibits ES* formation. Cryo-electron microscopy single particle analysis reveals a dynamic enzyme that becomes ordered upon formation of ES* in which extended acceptor stem pairing is unwound. Comparisons of structures with alternative ptRNAs reveals that once unwinding is completed RNase P primarily uses stacking interactions and shape complementarity to accommodate alternative sequences at its cleavage site. Our study reveals active site interactions and conformational changes that drive molecular recognition by RNase P and lays the foundation for understanding how binding interactions are linked to helix unwinding and catalysis. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26636.map.gz | 89.4 MB | EMDB map data format | |
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Header (meta data) | emd-26636-v30.xml emd-26636.xml | 11.2 KB 11.2 KB | Display Display | EMDB header |
Images | emd_26636.png | 53.7 KB | ||
Filedesc metadata | emd-26636.cif.gz | 5.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26636 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26636 | HTTPS FTP |
-Validation report
Summary document | emd_26636_validation.pdf.gz | 411.3 KB | Display | EMDB validaton report |
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Full document | emd_26636_full_validation.pdf.gz | 410.8 KB | Display | |
Data in XML | emd_26636_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | emd_26636_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26636 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26636 | HTTPS FTP |
-Related structure data
Related structure data | 7uo0MC 7uo1C 7uo2C 7uo5C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26636.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.058 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : E.coli RNase P holoenzyme with Mg2+
Entire | Name: E.coli RNase P holoenzyme with Mg2+ |
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Components |
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-Supramolecule #1: E.coli RNase P holoenzyme with Mg2+
Supramolecule | Name: E.coli RNase P holoenzyme with Mg2+ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Ribonuclease P protein component
Macromolecule | Name: Ribonuclease P protein component / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 13.818256 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MVKLAFPREL RLLTPSQFTF VFQQPQRAGT PQITILGRLN SLGHPRIGLT VAKKNVRRAH ERNRIKRLTR ESFRLRQHEL PAMDFVVVA KKGVADLDNR ALSEALEKLW RRHCRLARGS UniProtKB: Ribonuclease P protein component |
-Macromolecule #2: RNase P RNA
Macromolecule | Name: RNase P RNA / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 121.191891 KDa |
Sequence | String: GAAGCUGACC AGACAGUCGC CGCUUCGUCG UCGUCCUCUU CGGGGGAGAC GGGCGGAGGG GAGGAAAGUC CGGGCUCCAU AGGGCAGGG UGCCAGGUAA CGCCUGGGGG GGAAACCCAC GACCAGUGCA ACAGAGAGCA AACCGCCGAU GGCCCGCGCA A GCGGGAUC ...String: GAAGCUGACC AGACAGUCGC CGCUUCGUCG UCGUCCUCUU CGGGGGAGAC GGGCGGAGGG GAGGAAAGUC CGGGCUCCAU AGGGCAGGG UGCCAGGUAA CGCCUGGGGG GGAAACCCAC GACCAGUGCA ACAGAGAGCA AACCGCCGAU GGCCCGCGCA A GCGGGAUC AGGUAAGGGU GAAAGGGUGC GGUAAGAGCG CACCGCGCGG CUGGUAACAG UCCGUGGCAC GGUAAACUCC AC CCGGAGC AAGGCCAAAU AGGGGUUCAU AAGGUACGGC CCGUACUGAA CCCGGGUAGG CUGCUUGAGC CAGUGAGCGA UUG CUGGCC UAGAUGAAUG ACUGUCCACG ACAGAACCCG GCUUAUCGGU CAGUUUC GENBANK: GENBANK: CP053595.1 |
-Macromolecule #3: Precursor tRNA substrate G(-1) G(-2)
Macromolecule | Name: Precursor tRNA substrate G(-1) G(-2) / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 26.336613 KDa |
Sequence | String: UCUGGGGCUA CGUAGCUCAG UUGGUUAGAG CACAUCACUC AUAAUGAUGG GGUCACAGGU UCGAAUCCCG UCGUAGCCAC CA |
-Macromolecule #4: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 7 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.1 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: ab initio map generated by cryosparc |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 546283 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |