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Open data
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Basic information
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Title | E.coli RNaseP Holoenzyme with Mg2+ | |||||||||
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Function / homology | ![]() 3'-tRNA processing endoribonuclease activity / ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Huang W / Taylor DJ | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 96.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.5 KB 14.5 KB | Display Display | ![]() |
Images | ![]() | 29.3 KB | ||
Filedesc metadata | ![]() | 5.3 KB | ||
Others | ![]() ![]() | 176.2 MB 176.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7uo5MC ![]() 7uo0C ![]() 7uo1C ![]() 7uo2C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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Annotation | full map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.2132 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_26640_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_26640_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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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-#2 |
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Source (natural) | Organism: ![]() ![]() ![]() |
-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: ![]() |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 13.10237 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: KLAFPRELRL LTPSQFTFVF QQPQRAGTPQ ITILGRLNSL GHPRIGLTVA KKNVRRAHER NRIKRLTRES FRLRQHELPA MDFVVVAKK GVADLDNRAL SEALEKLWRR HCR UniProtKB: ![]() |
-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: ![]() ![]() ![]() |
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: ![]() |
-Macromolecule #3: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 7 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.1 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER / Details: ab initio map generated by cryosparc |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 576371 |