+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6778 | |||||||||
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Title | Large subunit of Toxoplasma gondii ribosome | |||||||||
Map data | ||||||||||
Sample |
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Keywords | parasitic ribosome / rRNA / rproteins / RIBOSOME | |||||||||
Biological species | Toxoplasma gondii (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.17 Å | |||||||||
Authors | Li Z / Guo Q | |||||||||
Citation | Journal: Cell Res / Year: 2017 Title: Cryo-EM structures of the 80S ribosomes from human parasites Trichomonas vaginalis and Toxoplasma gondii. Authors: Zhifei Li / Qiang Guo / Lvqin Zheng / Yongsheng Ji / Yi-Ting Xie / De-Hua Lai / Zhao-Rong Lun / Xun Suo / Ning Gao / Abstract: As an indispensable molecular machine universal in all living organisms, the ribosome has been selected by evolution to be the natural target of many antibiotics and small-molecule inhibitors. High- ...As an indispensable molecular machine universal in all living organisms, the ribosome has been selected by evolution to be the natural target of many antibiotics and small-molecule inhibitors. High-resolution structures of pathogen ribosomes are crucial for understanding the general and unique aspects of translation control in disease-causing microbes. With cryo-electron microscopy technique, we have determined structures of the cytosolic ribosomes from two human parasites, Trichomonas vaginalis and Toxoplasma gondii, at resolution of 3.2-3.4 Å. Although the ribosomal proteins from both pathogens are typical members of eukaryotic families, with a co-evolution pattern between certain species-specific insertions/extensions and neighboring ribosomal RNA (rRNA) expansion segments, the sizes of their rRNAs are sharply different. Very interestingly, rRNAs of T. vaginalis are in size comparable to prokaryotic counterparts, with nearly all the eukaryote-specific rRNA expansion segments missing. These structures facilitate the dissection of evolution path for ribosomal proteins and RNAs, and may aid in design of novel translation inhibitors. | |||||||||
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_6778.map.gz | 11.7 MB | EMDB map data format | |
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Header (meta data) | emd-6778-v30.xml emd-6778.xml | 51.1 KB 51.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6778_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_6778.png | 97.7 KB | ||
Masks | emd_6778_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-6778.cif.gz | 12.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6778 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6778 | HTTPS FTP |
-Validation report
Summary document | emd_6778_validation.pdf.gz | 487.9 KB | Display | EMDB validaton report |
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Full document | emd_6778_full_validation.pdf.gz | 487.5 KB | Display | |
Data in XML | emd_6778_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_6778_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6778 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6778 | HTTPS FTP |
-Related structure data
Related structure data | 5xxbMC 6780C 6784C 6788C 5xxuC 5xy3C 5xyiC 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_6778.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_6778_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Large subunit of Toxoplasma gondii ribosome
+Supramolecule #1: Large subunit of Toxoplasma gondii ribosome
+Macromolecule #1: 25S RNA
+Macromolecule #2: 5S RNA
+Macromolecule #3: 5.8S RNA
+Macromolecule #4: Ribosomal protein uL2
+Macromolecule #5: Ribosomal protein uL3
+Macromolecule #6: Ribosomal protein uL4
+Macromolecule #7: Ribosomal protein uL18
+Macromolecule #8: Ribosomal protein eL6
+Macromolecule #9: Ribosomal protein uL30
+Macromolecule #10: Ribosomal protein eL8
+Macromolecule #11: Ribosomal protein uL6
+Macromolecule #12: Ribosomal protein uL16
+Macromolecule #13: Ribosomal protein uL5
+Macromolecule #14: Ribosomal protein eL13
+Macromolecule #15: Ribosomal protein eL14
+Macromolecule #16: Ribosomal protein eL15
+Macromolecule #17: Ribosomal protein uL13
+Macromolecule #18: Ribosomal protein uL22
+Macromolecule #19: Ribosomal protein eL18
+Macromolecule #20: Ribosomal protein eL19
+Macromolecule #21: Ribosomal protein eL20
+Macromolecule #22: Ribosomal protein eL21
+Macromolecule #23: Ribosomal protein eL22
+Macromolecule #24: Ribosomal protein uL14
+Macromolecule #25: Ribosomal protein eL24
+Macromolecule #26: Ribosomal protein uL23
+Macromolecule #27: Ribosomal protein uL24
+Macromolecule #28: Ribosomal protein eL27
+Macromolecule #29: Ribosomal protein uL15
+Macromolecule #30: Ribosomal protein eL29
+Macromolecule #31: Ribosomal protein eL30
+Macromolecule #32: Ribosomal protein eL31
+Macromolecule #33: Ribosomal protein eL32
+Macromolecule #34: Ribosomal protein eL33
+Macromolecule #35: Ribosomal protein eL34
+Macromolecule #36: Ribosomal protein uL29
+Macromolecule #37: Ribosomal protein eL36
+Macromolecule #38: Ribosomal protein eL37
+Macromolecule #39: Ribosomal protein eL38
+Macromolecule #40: Ribosomal protein eL39
+Macromolecule #41: Ribosomal protein eL40
+Macromolecule #42: Ribosomal protein eL42
+Macromolecule #43: Ribosomal protein eL43
+Macromolecule #44: Ribosomal protein eL28
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |