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Yorodumi- PDB-7y18: Crystal structure of ribosomal ITS2 pre-rRNA processing complex f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7y18 | ||||||
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Title | Crystal structure of ribosomal ITS2 pre-rRNA processing complex from Saccharomyces cerevisiae | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / RNA processing / Nuclease | ||||||
Function / homology | Function and homology information polynucleotide 5'-hydroxyl-kinase activity / Las1 complex / nucleolar chromatin / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / maturation of 5.8S rRNA / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Major pathway of rRNA processing in the nucleolus and cytosol / termination of RNA polymerase I transcription / preribosome, large subunit precursor / RNA processing ...polynucleotide 5'-hydroxyl-kinase activity / Las1 complex / nucleolar chromatin / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / maturation of 5.8S rRNA / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Major pathway of rRNA processing in the nucleolus and cytosol / termination of RNA polymerase I transcription / preribosome, large subunit precursor / RNA processing / phosphorylation / maturation of LSU-rRNA / rRNA processing / endonuclease activity / nucleolus / mitochondrion / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.69 Å | ||||||
Authors | Chen, J. / Liu, L. | ||||||
Funding support | China, 1items
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Citation | Journal: Elife / Year: 2024 Title: Structural and mechanistic insights into ribosomal ITS2 RNA processing by nuclease-kinase machinery. Authors: Jiyun Chen / Hong Chen / Shanshan Li / Xiaofeng Lin / Rong Hu / Kaiming Zhang / Liang Liu / Abstract: Precursor ribosomal RNA (pre-rRNA) processing is a key step in ribosome biosynthesis and involves numerous RNases. A HEPN (higher eukaryote and prokaryote nucleotide binding) nuclease Las1 and a ...Precursor ribosomal RNA (pre-rRNA) processing is a key step in ribosome biosynthesis and involves numerous RNases. A HEPN (higher eukaryote and prokaryote nucleotide binding) nuclease Las1 and a polynucleotide kinase Grc3 assemble into a tetramerase responsible for rRNA maturation. Here, we report the structures of full-length and Las1-Grc3 complexes, and Las1. The Las1-Grc3 structures show that the central coiled-coil domain of Las1 facilitates pre-rRNA binding and cleavage, while the Grc3 C-terminal loop motif directly binds to the HEPN active center of Las1 and regulates pre-rRNA cleavage. Structural comparison between Las1 and Las1-Grc3 complex exhibits that Grc3 binding induces conformational rearrangements of catalytic residues associated with HEPN nuclease activation. Biochemical assays identify that Las1 processes pre-rRNA at the two specific sites (C2 and C2'), which greatly facilitates rRNA maturation. Our structures and specific pre-rRNA cleavage findings provide crucial insights into the mechanism and pathway of pre-rRNA processing in ribosome biosynthesis. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y18.cif.gz | 593.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y18.ent.gz | 470.4 KB | Display | PDB format |
PDBx/mmJSON format | 7y18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y18_validation.pdf.gz | 522.3 KB | Display | wwPDB validaton report |
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Full document | 7y18_full_validation.pdf.gz | 918.8 KB | Display | |
Data in XML | 7y18_validation.xml.gz | 158.8 KB | Display | |
Data in CIF | 7y18_validation.cif.gz | 205.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/7y18 ftp://data.pdbj.org/pub/pdb/validation_reports/y1/7y18 | HTTPS FTP |
-Related structure data
Related structure data | 7y16C 7y17C 8j5yC 8j60C 6of4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 72342.430 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: GRC3, YLL035W / Production host: Escherichia coli K-12 (bacteria) References: UniProt: Q07845, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: Protein | Mass: 59435.332 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: LAS1, YKR063C / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P36146 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.71 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 2% tacsimate, pH 7.0, 0.1 M imidazole, pH 7.0, 2% 2-propanole, and 9% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 13, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 36773 / % possible obs: 98.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 43.42 Å2 / Rpim(I) all: 0.157 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 3.5→3.56 Å / Num. unique obs: 2594 / Rpim(I) all: 0.585 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6OF4 Resolution: 3.69→48.63 Å / SU ML: 0.5523 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.5715 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 94.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.69→48.63 Å
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Refine LS restraints |
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LS refinement shell |
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