[English] 日本語
![](img/lk-miru.gif)
- PDB-8cbo: Structure of human mitochondrial MRPP1-MRPP2 in complex with mito... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8cbo | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of human mitochondrial MRPP1-MRPP2 in complex with mitochondrial pre-tRNA-Ile | ||||||
![]() |
| ||||||
![]() | RNA BINDING PROTEIN / RNA maturation / RNA modification / mitochondrial tRNA / RNA methyltransferase / MRPP1 / MRPP2 / MRPP3 / m6A / RNA binding / RNA recognition | ||||||
Function / homology | ![]() mitochondrial RNA 5'-end processing / mitochondrial tRNA processing / brexanolone metabolic process / isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity / rRNA processing in the mitochondrion / tRNA (adenine9-N1)-methyltransferase / mitochondrial tRNA methylation ...mitochondrial RNA 5'-end processing / mitochondrial tRNA processing / brexanolone metabolic process / isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase / 3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity / rRNA processing in the mitochondrion / tRNA (adenine9-N1)-methyltransferase / mitochondrial tRNA methylation / tRNA (adenine(9)-N1)-methyltransferase activity / tRNA processing in the mitochondrion / tRNA (guanine9-N1)-methyltransferase / mitochondrial ribonuclease P complex / tRNA (guanosine(9)-N1)-methyltransferase activity / mitochondrial tRNA 5'-end processing / chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity / mitochondrial tRNA 3'-end processing / tRNA modification in the mitochondrion / 7alpha-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NAD+) activity / cholate 7-alpha-dehydrogenase activity / C21-steroid hormone metabolic process / testosterone dehydrogenase [NAD(P)+] activity / tRNA methyltransferase complex / 3-hydroxyacyl-CoA dehydrogenase / isoleucine catabolic process / 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+) / 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / 3-hydroxyacyl-CoA dehydrogenase activity / testosterone dehydrogenase (NAD+) activity / bile acid biosynthetic process / Branched-chain amino acid catabolism / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / positive regulation of mitochondrial translation / estrogen metabolic process / fatty acid beta-oxidation / mitochondrial nucleoid / androgen metabolic process / Mitochondrial protein degradation / Transferases; Transferring one-carbon groups; Methyltransferases / mitochondrion organization / fatty acid metabolic process / lipid metabolic process / mRNA processing / protein homotetramerization / tRNA binding / mitochondrial matrix / mitochondrion / RNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
![]() | MEYNIER, V. / HARDWICK, S. / CATALA, M. / ROSKE, J. / OERUM, S. / CHIRGADZE, D. / BARRAUD, P. / LUISI, B. / TISNE, C. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural basis for human mitochondrial tRNA maturation. Authors: Vincent Meynier / Steven W Hardwick / Marjorie Catala / Johann J Roske / Stephanie Oerum / Dimitri Y Chirgadze / Pierre Barraud / Wyatt W Yue / Ben F Luisi / Carine Tisné / ![]() ![]() Abstract: The human mitochondrial genome is transcribed into two RNAs, containing mRNAs, rRNAs and tRNAs, all dedicated to produce essential proteins of the respiratory chain. The precise excision of tRNAs by ...The human mitochondrial genome is transcribed into two RNAs, containing mRNAs, rRNAs and tRNAs, all dedicated to produce essential proteins of the respiratory chain. The precise excision of tRNAs by the mitochondrial endoribonucleases (mt-RNase), P and Z, releases all RNA species from the two RNA transcripts. The tRNAs then undergo 3'-CCA addition. In metazoan mitochondria, RNase P is a multi-enzyme assembly that comprises the endoribonuclease PRORP and a tRNA methyltransferase subcomplex. The requirement for this tRNA methyltransferase subcomplex for mt-RNase P cleavage activity, as well as the mechanisms of pre-tRNA 3'-cleavage and 3'-CCA addition, are still poorly understood. Here, we report cryo-EM structures that visualise four steps of mitochondrial tRNA maturation: 5' and 3' tRNA-end processing, methylation and 3'-CCA addition, and explain the defined sequential order of the tRNA processing steps. The methyltransferase subcomplex recognises the pre-tRNA in a distinct mode that can support tRNA-end processing and 3'-CCA addition, likely resulting from an evolutionary adaptation of mitochondrial tRNA maturation complexes to the structurally-fragile mitochondrial tRNAs. This subcomplex can also ensure a tRNA-folding quality-control checkpoint before the sequential docking of the maturation enzymes. Altogether, our study provides detailed molecular insight into RNA-transcript processing and tRNA maturation in human mitochondria. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 271.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 213.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 16547MC ![]() 8cbkC ![]() 8cblC ![]() 8cbmC C: citing same article ( M: map data used to model this data |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 26342.254 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q99714, 3-hydroxyacyl-CoA dehydrogenase, 17beta-estradiol 17-dehydrogenase, 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+), 3-hydroxy-2-methylbutyryl-CoA dehydrogenase, ...References: UniProt: Q99714, 3-hydroxyacyl-CoA dehydrogenase, 17beta-estradiol 17-dehydrogenase, 3alpha(17beta)-hydroxysteroid dehydrogenase (NAD+), 3-hydroxy-2-methylbutyryl-CoA dehydrogenase, 3alpha(or 20beta)-hydroxysteroid dehydrogenase, 7alpha-hydroxysteroid dehydrogenase #2: Protein | | Mass: 24857.826 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q7L0Y3, Transferases; Transferring one-carbon groups; Methyltransferases, tRNA (adenine9-N1)-methyltransferase, tRNA (guanine9-N1)-methyltransferase #3: RNA chain | | Mass: 25118.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() #4: Chemical | ChemComp-NAD / #5: Chemical | ChemComp-SAH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.170 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
| ||||||||||||||||||||||||
Source (recombinant) |
| ||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: DIFFRACTION / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 900 nm |
Image recording | Electron dose: 40.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-
Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 141653 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 133.7 / Protocol: AB INITIO MODEL / Target criteria: Cross-correlation coefficient |