[English] 日本語
![](img/lk-miru.gif)
- PDB-7am2: Intermediate assembly of the Large subunit from Leishmania major ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7am2 | ||||||
---|---|---|---|---|---|---|---|
Title | Intermediate assembly of the Large subunit from Leishmania major mitochondrial ribosome | ||||||
![]() |
| ||||||
![]() | RIBOSOME / Mitochondria / Kinetoplastid | ||||||
Function / homology | ![]() pseudouridine synthesis / enzyme-directed rRNA pseudouridine synthesis / pseudouridine synthase activity / negative regulation of ribosome biogenesis / kinetoplast / RNA methyltransferase activity / nuclear lumen / mitochondrial large ribosomal subunit / ciliary plasm / mitochondrial ribosome ...pseudouridine synthesis / enzyme-directed rRNA pseudouridine synthesis / pseudouridine synthase activity / negative regulation of ribosome biogenesis / kinetoplast / RNA methyltransferase activity / nuclear lumen / mitochondrial large ribosomal subunit / ciliary plasm / mitochondrial ribosome / cyclosporin A binding / mitochondrial translation / ribosomal large subunit binding / : / acyl binding / acyl carrier activity / RNA processing / helicase activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / fatty acid biosynthetic process / rRNA processing / large ribosomal subunit / protein folding / ribosome biogenesis / large ribosomal subunit rRNA binding / nucleic acid binding / cytosolic large ribosomal subunit / rRNA binding / negative regulation of translation / hydrolase activity / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / intracellular membrane-bounded organelle / GTPase activity / mRNA binding / GTP binding / mitochondrion / RNA binding / ATP binding / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
![]() | Soufari, H. / Waltz, F. / Parrot, C. / Bochler, A. / Hashem, Y. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structure of the mature kinetoplastids mitoribosome and insights into its large subunit biogenesis. Authors: Heddy Soufari / Florent Waltz / Camila Parrot / Stéphanie Durrieu-Gaillard / Anthony Bochler / Lauriane Kuhn / Marie Sissler / Yaser Hashem / ![]() Abstract: Kinetoplastids are unicellular eukaryotic parasites responsible for such human pathologies as Chagas disease, sleeping sickness, and leishmaniasis. They have a single large mitochondrion, essential ...Kinetoplastids are unicellular eukaryotic parasites responsible for such human pathologies as Chagas disease, sleeping sickness, and leishmaniasis. They have a single large mitochondrion, essential for the parasite survival. In kinetoplastid mitochondria, most of the molecular machineries and gene expression processes have significantly diverged and specialized, with an extreme example being their mitochondrial ribosomes. These large complexes are in charge of translating the few essential mRNAs encoded by mitochondrial genomes. Structural studies performed in already highlighted the numerous peculiarities of these mitoribosomes and the maturation of their small subunit. However, several important aspects mainly related to the large subunit (LSU) remain elusive, such as the structure and maturation of its ribosomal RNA. Here we present a cryo-electron microscopy study of the protozoans and mitoribosomes. For both species, we obtained the structure of their mature mitoribosomes, complete rRNA of the LSU, as well as previously unidentified ribosomal proteins. In addition, we introduce the structure of an LSU assembly intermediate in the presence of 16 identified maturation factors. These maturation factors act on both the intersubunit and the solvent sides of the LSU, where they refold and chemically modify the rRNA and prevent early translation before full maturation of the LSU. | ||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 3.4 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 384 KB | Display | |
Data in CIF | ![]() | 646.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11821MC ![]() 7aihC ![]() 7aneC ![]() 7aorC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
+Protein , 64 types, 65 molecules ABCFGIJKLMNOQRSTVZBACAUABBCBBKBQBNBEAtAuAe...
-Putative ribosomal protein ... , 2 types, 2 molecules EBO
#4: Protein | Mass: 40274.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#29: Protein | Mass: 21633.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Peptidyl-prolyl cis-trans ... , 2 types, 2 molecules BHBl
#46: Protein | Mass: 25314.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#54: Protein | Mass: 28924.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-G domain-containing ... , 2 types, 2 molecules BTBV
#61: Protein | Mass: 51661.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#64: Protein | Mass: 86927.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein/peptide , 3 types, 3 molecules U7U1U2
#65: Protein/peptide | Mass: 3422.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#67: Protein/peptide | Mass: 3287.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#72: Protein/peptide | Mass: 2647.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-RNA chain , 4 types, 4 molecules 1R1R2R5
#73: RNA chain | Mass: 6061920.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|---|
#74: RNA chain | Mass: 896.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#75: RNA chain | Mass: 10670.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#76: RNA chain | Mass: 1485.872 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 2 types, 2 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/ATP.gif)
#78: Chemical | ChemComp-GTP / |
---|---|
#79: Chemical | ChemComp-ATP / |
-Details
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 | Name: Leishmania mitochondrial ribosome / Type: RIBOSOME Entity ID: #1, #10-#19, #2, #20-#29, #3, #30-#39, #4, #40-#49, #5, #50-#59, #6, #60-#69, #7, #70-#77, #8-#9 Source: NATURAL |
---|---|
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 60 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-
Processing
EM software |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59200 / Symmetry type: POINT |