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Yorodumi- EMDB-8361: Structure and assembly model for the Trypanosoma cruzi 60S riboso... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8361 | ||||||||||||||||||
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Title | Structure and assembly model for the Trypanosoma cruzi 60S ribosomal subunit | ||||||||||||||||||
Map data | Structure and assembly model for the Trypanosoma cruzi 60S ribosomal subunit | ||||||||||||||||||
Sample |
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Function / homology | Function and homology information maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nucleosome assembly / nucleosome / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / membrane => GO:0016020 / rRNA binding / ribosome / structural constituent of ribosome ...maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nucleosome assembly / nucleosome / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / membrane => GO:0016020 / rRNA binding / ribosome / structural constituent of ribosome / translation / DNA binding / RNA binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.54 Å | ||||||||||||||||||
Authors | Liu Z / Gutierrez-Vargas C / Wei J / Grassucci RA / Ramesh M / Espina N / Sun M / Tutuncuoglu B / Madison-Antenucci S / Woolford Jr JL ...Liu Z / Gutierrez-Vargas C / Wei J / Grassucci RA / Ramesh M / Espina N / Sun M / Tutuncuoglu B / Madison-Antenucci S / Woolford Jr JL / Tong L / Frank J | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2016 Title: Structure and assembly model for the Trypanosoma cruzi 60S ribosomal subunit. Authors: Zheng Liu / Cristina Gutierrez-Vargas / Jia Wei / Robert A Grassucci / Madhumitha Ramesh / Noel Espina / Ming Sun / Beril Tutuncuoglu / Susan Madison-Antenucci / John L Woolford / Liang Tong / Joachim Frank / Abstract: Ribosomes of trypanosomatids, a family of protozoan parasites causing debilitating human diseases, possess multiply fragmented rRNAs that together are analogous to 28S rRNA, unusually large rRNA ...Ribosomes of trypanosomatids, a family of protozoan parasites causing debilitating human diseases, possess multiply fragmented rRNAs that together are analogous to 28S rRNA, unusually large rRNA expansion segments, and r-protein variations compared with other eukaryotic ribosomes. To investigate the architecture of the trypanosomatid ribosomes, we determined the 2.5-Å structure of the Trypanosoma cruzi ribosome large subunit by single-particle cryo-EM. Examination of this structure and comparative analysis of the yeast ribosomal assembly pathway allowed us to develop a stepwise assembly model for the eight pieces of the large subunit rRNAs and a number of ancillary "glue" proteins. This model can be applied to the characterization of Trypanosoma brucei and Leishmania spp. ribosomes as well. Together with other details, our atomic-level structure may provide a foundation for structure-based design of antitrypanosome drugs. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8361.map.gz | 43.2 MB | EMDB map data format | |
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Header (meta data) | emd-8361-v30.xml emd-8361.xml | 54.1 KB 54.1 KB | Display Display | EMDB header |
Images | emd_8361.png | 769.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8361 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8361 | HTTPS FTP |
-Related structure data
Related structure data | 5t5hMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8361.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure and assembly model for the Trypanosoma cruzi 60S ribosomal subunit | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.045 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : trypanosoma cruzi 60S ribosomal subunit
+Supramolecule #1: trypanosoma cruzi 60S ribosomal subunit
+Macromolecule #1: RNA LARGE SUBUNIT ALPHA
+Macromolecule #2: RNA LARGE SUBUNIT BETA
+Macromolecule #3: 5.8S rRNA
+Macromolecule #4: 5S rRNA
+Macromolecule #5: srRNA1
+Macromolecule #6: srRNA3
+Macromolecule #7: srRNA2
+Macromolecule #8: srRNA4
+Macromolecule #9: 60S ribosomal protein L18
+Macromolecule #10: 60S ribosomal protein L11
+Macromolecule #11: 60S ribosomal protein L13
+Macromolecule #12: 60S ribosomal protein L13a
+Macromolecule #13: 40S ribosomal protein L14
+Macromolecule #14: Ribosomal protein L15
+Macromolecule #15: 60S ribosomal protein L17
+Macromolecule #16: 60S ribosomal protein L18a
+Macromolecule #17: Ribosomal protein L19-like protein
+Macromolecule #18: Ribosomal protein L21E (60S)
+Macromolecule #19: 60S ribosomal protein L22
+Macromolecule #20: 60S ribosomal protein L23
+Macromolecule #21: 60S ribosomal protein L23a
+Macromolecule #22: Ribosomal protein L24
+Macromolecule #23: 60S ribosomal protein L26
+Macromolecule #24: Ribosomal protein L27
+Macromolecule #25: 60S ribosomal protein L27A/L29
+Macromolecule #26: 60S ribosomal protein L28
+Macromolecule #27: Ribosomal protein L29
+Macromolecule #28: 60S ribosomal protein L2
+Macromolecule #29: Ribosomal protein L13
+Macromolecule #30: 60S ribosomal protein L30
+Macromolecule #31: 60S ribosomal subunit protein L31
+Macromolecule #32: 60S ribosomal protein L32
+Macromolecule #33: 60S ribosomal protein L34
+Macromolecule #34: 60S ribosomal protein L35
+Macromolecule #35: Ribosomal protein L35A
+Macromolecule #36: Ribosomal protein L36
+Macromolecule #37: Ribosomal protein L37
+Macromolecule #38: 60S ribosomal protein L37a
+Macromolecule #39: Ribosomal protein L38
+Macromolecule #40: Ribosomal protein L39
+Macromolecule #41: 60S ribosomal protein L4
+Macromolecule #42: 60S ribosomal protein L44
+Macromolecule #43: 60S ribosomal protein L5
+Macromolecule #44: 60S ribosomal protein L6
+Macromolecule #45: 60S ribosomal protein L7
+Macromolecule #46: Ribosomal protein L7a-like protein
+Macromolecule #47: MAGNESIUM ION
+Macromolecule #48: ZINC ION
+Macromolecule #49: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Grid | Model: Quantfoil / Material: COPPER / Mesh: 400 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 27.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 235000 |
-Atomic model buiding 1
Refinement | Space: REAL / Overall B value: 56 |
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Output model | PDB-5t5h: |