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Yorodumi- PDB-6ah3: Cryo-EM structure of yeast Ribonuclease P with pre-tRNA substrate -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ah3 | ||||||
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Title | Cryo-EM structure of yeast Ribonuclease P with pre-tRNA substrate | ||||||
Components |
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Keywords | HYDROLASE/RNA / Ribonuclease P / RNA-protein complex / HYDROLASE-RNA complex | ||||||
Function / homology | Function and homology information ribonuclease MRP activity / nuclear-transcribed mRNA catabolic process, RNase MRP-dependent / intronic box C/D snoRNA processing / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / ribonuclease P / ribonuclease P activity / rRNA primary transcript binding ...ribonuclease MRP activity / nuclear-transcribed mRNA catabolic process, RNase MRP-dependent / intronic box C/D snoRNA processing / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / ribonuclease P / ribonuclease P activity / rRNA primary transcript binding / tRNA 5'-leader removal / telomerase holoenzyme complex / maturation of 5.8S rRNA / tRNA processing / rRNA processing / RNA binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å | ||||||
Authors | Lan, P. / Tan, M. / Wu, J. / Lei, M. | ||||||
Citation | Journal: Science / Year: 2018 Title: Structural insight into precursor tRNA processing by yeast ribonuclease P. Authors: Pengfei Lan / Ming Tan / Yuebin Zhang / Shuangshuang Niu / Juan Chen / Shaohua Shi / Shuwan Qiu / Xuejuan Wang / Xiangda Peng / Gang Cai / Hong Cheng / Jian Wu / Guohui Li / Ming Lei / Abstract: Ribonuclease P (RNase P) is a universal ribozyme responsible for processing the 5'-leader of pre-transfer RNA (pre-tRNA). Here, we report the 3.5-angstrom cryo-electron microscopy structures of ...Ribonuclease P (RNase P) is a universal ribozyme responsible for processing the 5'-leader of pre-transfer RNA (pre-tRNA). Here, we report the 3.5-angstrom cryo-electron microscopy structures of RNase P alone and in complex with pre-tRNA The protein components form a hook-shaped architecture that wraps around the RNA and stabilizes RNase P into a "measuring device" with two fixed anchors that recognize the L-shaped pre-tRNA. A universally conserved uridine nucleobase and phosphate backbone in the catalytic center together with the scissile phosphate and the O3' leaving group of pre-tRNA jointly coordinate two catalytic magnesium ions. Binding of pre-tRNA induces a conformational change in the catalytic center that is required for catalysis. Moreover, simulation analysis suggests a two-metal-ion S2 reaction pathway of pre-tRNA cleavage. These results not only reveal the architecture of yeast RNase P but also provide a molecular basis of how the 5'-leader of pre-tRNA is processed by eukaryotic RNase P. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ah3.cif.gz | 638.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ah3.ent.gz | 519.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ah3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ah3_validation.pdf.gz | 949.3 KB | Display | wwPDB validaton report |
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Full document | 6ah3_full_validation.pdf.gz | 995.5 KB | Display | |
Data in XML | 6ah3_validation.xml.gz | 74.1 KB | Display | |
Data in CIF | 6ah3_validation.cif.gz | 115.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/6ah3 ftp://data.pdbj.org/pub/pdb/validation_reports/ah/6ah3 | HTTPS FTP |
-Related structure data
Related structure data | 9622MC 9616C 6agbC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Ribonuclease P ... , 2 types, 2 molecules AK
#1: RNA chain | Mass: 118857.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: GenBank: 1163001456 |
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#10: Protein | Mass: 16375.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P40571, ribonuclease P |
-Ribonucleases P/MRP protein subunit ... , 5 types, 5 molecules BCFGH
#2: Protein | Mass: 100559.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P41812, ribonuclease P |
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#3: Protein | Mass: 22643.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P53833 |
#6: Protein | Mass: 18234.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P53218, ribonuclease P |
#7: Protein | Mass: 15844.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P38291, ribonuclease P |
#8: Protein | Mass: 15530.351 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P38208, ribonuclease P |
-Ribonuclease P/MRP protein subunit ... , 2 types, 3 molecules EIJ
#5: Protein | Mass: 19601.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P28005, ribonuclease P |
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#9: Protein | Mass: 32270.262 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P38786, ribonuclease P |
-Protein / RNA chain , 2 types, 2 molecules DT
#11: RNA chain | Mass: 25830.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: in vitro transcription / Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Plasmid: pGlms / Production host: Saccharomyces cerevisiae (brewer's yeast) |
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#4: Protein | Mass: 32933.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P38336 |
-Non-polymers , 2 types, 3 molecules
#12: Chemical | #13: Chemical | ChemComp-ZN / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Plasmid: pGlms | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.5625 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176896 / Symmetry type: POINT |