+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6784 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Large subunit of Trichomonas vaginalis ribosome | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | Trichomonas vaginalis ribosome / rRNA / rprotein / RIBOSOME | |||||||||
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 / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / 5S 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 / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Trichomonas vaginalis (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6784.map.gz | 11.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-6784-v30.xml emd-6784.xml | 53.2 KB 53.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6784_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_6784.png | 91.3 KB | ||
Masks | emd_6784_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-6784.cif.gz | 11.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6784 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6784 | HTTPS FTP |
-Validation report
Summary document | emd_6784_validation.pdf.gz | 462.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_6784_full_validation.pdf.gz | 461.8 KB | Display | |
Data in XML | emd_6784_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_6784_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6784 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6784 | HTTPS FTP |
-Related structure data
Related structure data | 5xy3MC 6778C 6780C 6788C 5xxbC 5xxuC 5xyiC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_6784.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_6784_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : Large subunit of Trichomonas vaginalis ribosome
+Supramolecule #1: Large subunit of Trichomonas vaginalis ribosome
+Macromolecule #1: 25S ribosomal RNA
+Macromolecule #2: 5S ribosomal RNA
+Macromolecule #3: 5.8S ribosomal RNA
+Macromolecule #4: Ribosomal protein L8, putative
+Macromolecule #5: Uncharacterized protein
+Macromolecule #6: Ribosomal protein, putative
+Macromolecule #7: Ribosomal protein L5
+Macromolecule #8: 60S ribosomal protein L6, putative
+Macromolecule #9: Ribosomal protein L30p/L7e, putative
+Macromolecule #10: Ribosomal protein L7Ae, putative
+Macromolecule #11: Ribosomal protein L6, putative
+Macromolecule #12: Ribosomal protein, putative
+Macromolecule #13: 60S ribosomal protein L11, putative
+Macromolecule #14: Ribosomal protein L13e, putative
+Macromolecule #15: Ribosomal protein L14, putative
+Macromolecule #16: Ribosomal protein L15
+Macromolecule #17: Ribosomal protein L13, putative
+Macromolecule #18: Ribosomal protein L22, putative
+Macromolecule #19: 60S ribosomal protein L18, putative
+Macromolecule #20: 60S ribosomal protein L19-3, putative
+Macromolecule #21: 60S ribosomal protein L18a
+Macromolecule #22: Ribosomal protein L21e, putative
+Macromolecule #23: 60S ribosomal protein L22-1, putative
+Macromolecule #24: 60S ribosomal protein L23, putative
+Macromolecule #25: Ribosomal protein L24e, putative
+Macromolecule #26: Ribosomal protein L23, putative
+Macromolecule #27: Ribosomal protein L24, putative
+Macromolecule #28: Ribosomal protein L27e, putative
+Macromolecule #29: Uncharacterized protein
+Macromolecule #30: 60S ribosomal protein L29
+Macromolecule #31: 60S ribosomal protein L30, putative
+Macromolecule #32: Ribosomal protein L31e, putative
+Macromolecule #33: Ribosomal protein L32, putative
+Macromolecule #34: Ribosomal protein L35Ae, putative
+Macromolecule #35: Ribosomal protein L34e, putative
+Macromolecule #36: Ribosomal protein L29, putative
+Macromolecule #37: Ribosomal protein L36e, putative
+Macromolecule #38: Ribosomal protein L37
+Macromolecule #39: Ribosomal protein L38e, putative
+Macromolecule #40: 60S ribosomal protein L39, putative
+Macromolecule #41: Ubiquitin, putative
+Macromolecule #42: 60S ribosomal protein L44, putative
+Macromolecule #43: Uncharacterized protein
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |