+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33735 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of CjLas1-Grc3 complex | |||||||||
Map data | Cryo-EM structure of CjLas1-Grc3 complex | |||||||||
Sample |
| |||||||||
Keywords | endoribonuclease / ribosome biosynthesis / Las1 / Grc3 / RNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information polynucleotide 5'-hydroxyl-kinase activity / Las1 complex / 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) / preribosome, large subunit precursor / maturation of LSU-rRNA / endonuclease activity / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | Cyberlindnera jadinii (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.39 Å | |||||||||
Authors | Chen J / Chen H / Li S / Lin X / Hu R / Zhang K / Liu L | |||||||||
Funding support | China, 1 items
| |||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_33735.map.gz | 136.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-33735-v30.xml emd-33735.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | emd_33735.png | 38.3 KB | ||
Filedesc metadata | emd-33735.cif.gz | 4 KB | ||
Others | emd_33735_half_map_1.map.gz emd_33735_half_map_2.map.gz | 134.3 MB 134.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33735 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33735 | HTTPS FTP |
-Validation report
Summary document | emd_33735_validation.pdf.gz | 761.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_33735_full_validation.pdf.gz | 761 KB | Display | |
Data in XML | emd_33735_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | emd_33735_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33735 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33735 | HTTPS FTP |
-Related structure data
Related structure data | 8j60MC 7y16C 7y17C 7y18C 8j5yC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_33735.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cryo-EM structure of CjLas1-Grc3 complex | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: Half map 2
File | emd_33735_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 1
File | emd_33735_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Cryo-EM structure of CjLas1-Grc3 complex
Entire | Name: Cryo-EM structure of CjLas1-Grc3 complex |
---|---|
Components |
|
-Supramolecule #1: Cryo-EM structure of CjLas1-Grc3 complex
Supramolecule | Name: Cryo-EM structure of CjLas1-Grc3 complex / type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Cyberlindnera jadinii (fungus) |
Molecular weight | Theoretical: 400 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
---|---|
Buffer | pH: 7.5 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |