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Open data
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Basic information
Entry | Database: PDB / ID: 7y16 | ||||||
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Title | Crystal structure of rRNA-processing protein Las1 | ||||||
![]() | LAS1 protein | ||||||
![]() | RNA BINDING PROTEIN / RNA processing / Nuclease | ||||||
Function / homology | Las1 / Las1-like / Las1 complex / maturation of 5.8S rRNA / preribosome, large subunit precursor / maturation of LSU-rRNA / endonuclease activity / LAS1 protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, J. / Liu, L. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.9 KB | Display | ![]() |
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PDB format | ![]() | 81.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.4 KB | Display | ![]() |
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Full document | ![]() | 468.7 KB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 30.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7y17C ![]() 7y18C ![]() 8j5yC ![]() 8j60C ![]() 6of4S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18260.857 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 18201 / CBS 1600 / BCRC 20928 / JCM 3617 / NBRC 0987 / NRRL Y-1542 Gene: LAS1, BN1211_1791 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.07 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-HCl, pH 8.0, 0.2 M MgCl2, and 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 44296 / % possible obs: 97.7 % / Redundancy: 10.1 % / Biso Wilson estimate: 18.13 Å2 / Rpim(I) all: 0.033 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.8→1.83 Å / Num. unique obs: 2147 / Rpim(I) all: 0.305 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6OF4 Resolution: 1.8→48.98 Å / SU ML: 0.189 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 21.9489 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: 23.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→48.98 Å
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Refine LS restraints |
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LS refinement shell |
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