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Yorodumi- PDB-3jcs: 2.8 Angstrom cryo-EM structure of the large ribosomal subunit fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jcs | ||||||
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Title | 2.8 Angstrom cryo-EM structure of the large ribosomal subunit from the eukaryotic parasite Leishmania | ||||||
Components |
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Keywords | RIBOSOME / Leishmania donovani / the large ribosomal subunit / eukaryotic parasite | ||||||
Function / homology | Function and homology information protein-RNA complex assembly / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosome biogenesis / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding ...protein-RNA complex assembly / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosome biogenesis / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Leishmania donovani (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Shalev-Benami, M. / Zhang, Y. / Matzov, D. / Halfon, Y. / Zackay, A. / Rozenberg, H. / Zimmerman, E. / Bashan, A. / Jaffe, C.L. / Yonath, A. / Skiniotis, G. | ||||||
Citation | Journal: Cell Rep / Year: 2016 Title: 2.8-Å Cryo-EM Structure of the Large Ribosomal Subunit from the Eukaryotic Parasite Leishmania. Authors: Moran Shalev-Benami / Yan Zhang / Donna Matzov / Yehuda Halfon / Arie Zackay / Haim Rozenberg / Ella Zimmerman / Anat Bashan / Charles L Jaffe / Ada Yonath / Georgios Skiniotis / Abstract: Leishmania is a single-cell eukaryotic parasite of the Trypanosomatidae family, whose members cause an array of tropical diseases. The often fatal outcome of infections, lack of effective vaccines, ...Leishmania is a single-cell eukaryotic parasite of the Trypanosomatidae family, whose members cause an array of tropical diseases. The often fatal outcome of infections, lack of effective vaccines, limited selection of therapeutic drugs, and emerging resistant strains, underline the need to develop strategies to combat these pathogens. The Trypanosomatid ribosome has recently been highlighted as a promising therapeutic target due to structural features that are distinct from other eukaryotes. Here, we present the 2.8-Å resolution structure of the Leishmania donovani large ribosomal subunit (LSU) derived from a cryo-EM map, further enabling the structural observation of eukaryotic rRNA modifications that play a significant role in ribosome assembly and function. The structure illustrates the unique fragmented nature of leishmanial LSU rRNA and highlights the irregular distribution of rRNA modifications in Leishmania, a characteristic with implications for anti-parasitic drug development. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3jcs.cif.gz | 2.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3jcs.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 3jcs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jcs_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3jcs_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3jcs_validation.xml.gz | 187.8 KB | Display | |
Data in CIF | 3jcs_validation.cif.gz | 325.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/3jcs ftp://data.pdbj.org/pub/pdb/validation_reports/jc/3jcs | HTTPS FTP |
-Related structure data
Related structure data | 6583MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 6 types, 6 molecules 135678
#1: RNA chain | Mass: 576874.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) |
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#3: RNA chain | Mass: 68191.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) |
#5: RNA chain | Mass: 42869.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) |
#6: RNA chain | Mass: 24254.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) |
#7: RNA chain | Mass: 54961.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) |
#8: RNA chain | Mass: 38840.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) |
-26S delta ribosomal ... , 2 types, 2 molecules 24
#2: RNA chain | Mass: 492600.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) |
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#4: RNA chain | Mass: 59130.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania donovani (eukaryote) |
+Ribosomal protein ... , 40 types, 40 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...
-Non-polymers , 2 types, 253 molecules
#49: Chemical | ChemComp-MG / #50: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Buffer solution | Name: 20 mM HEPES-KOH, pH 7.6, 100 mM KOAc, 10 mM Mg(OAc)2, 10 mM NH4OAc, 1 mM DTT pH: 7.6 Details: 20 mM HEPES-KOH, pH 7.6, 100 mM KOAc, 10 mM Mg(OAc)2, 10 mM NH4OAc, 1 mM DTT | ||||||||||||||||||||||||||||||||
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||
Specimen support | Details: 25 seconds on glow-discharged holey carbon grids (Quantifoil R2/2) coated with continuous thin carbon film | ||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV). |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Jul 7, 2015 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 29000 X / Calibrated magnification: 25000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 600 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Method: Maximum likelihood / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107134 / Nominal pixel size: 1 Å / Actual pixel size: 1 Å / Symmetry type: POINT | ||||||||||||||||||||||||
Displacement parameters | Biso max: 167 Å2 / Biso mean: 39.2037 Å2 / Biso min: 2.89 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST
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Refine LS restraints |
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