+Open data
-Basic information
Entry | Database: PDB / ID: 5xy3 | ||||||
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Title | Large subunit of Trichomonas vaginalis ribosome | ||||||
Components |
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Keywords | RIBOSOME / Trichomonas vaginalis ribosome / rRNA / rprotein | ||||||
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) / assembly of large subunit precursor of preribosome / ribosomal large subunit biogenesis / ribosomal large subunit assembly / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / 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) / assembly of large subunit precursor of preribosome / ribosomal large subunit biogenesis / ribosomal large subunit assembly / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / mRNA binding / ubiquitin protein ligase binding / RNA binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Trichomonas vaginalis (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Li, Z. / Guo, Q. / Zheng, L. / Ji, Y. / Xie, Y. / Lai, D. / Lun, Z. / Suo, X. / Gao, N. | ||||||
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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5xy3.cif.gz | 2.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5xy3.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5xy3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xy3_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5xy3_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5xy3_validation.xml.gz | 174.2 KB | Display | |
Data in CIF | 5xy3_validation.cif.gz | 297.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/5xy3 ftp://data.pdbj.org/pub/pdb/validation_reports/xy/5xy3 | HTTPS FTP |
-Related structure data
Related structure data | 6784MC 6778C 6780C 6788C 5xxbC 5xxuC 5xyiC 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 , 3 types, 3 molecules 134
#1: RNA chain | Mass: 892223.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: GenBank: 7243609 |
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#2: RNA chain | Mass: 37963.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: GenBank: 68235680 |
#3: RNA chain | Mass: 52173.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: GenBank: 461415 |
+Ribosomal protein ... , 23 types, 23 molecules ADFGHLMNOPTWXYZdefghijk
-Uncharacterized ... , 3 types, 3 molecules Bap
#5: Protein | Mass: 46904.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DD62 |
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#29: Protein | Mass: 17006.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DHU7 |
#43: Protein | Mass: 10051.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DEM7 |
-Ribosomal protein, ... , 2 types, 2 molecules CI
#6: Protein | Mass: 40320.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2E4D0 |
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#12: Protein | Mass: 23800.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2FVZ6 |
-60S ribosomal protein ... , 11 types, 11 molecules EJQRSUVbclo
#8: Protein | Mass: 16045.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2FXW1 |
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#13: Protein | Mass: 19373.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2E7L8 |
#19: Protein | Mass: 21122.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2D7Q5 |
#20: Protein | Mass: 21056.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2D8G1 |
#21: Protein | Mass: 19853.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2EP03 |
#23: Protein | Mass: 12237.054 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DNV5 |
#24: Protein | Mass: 14840.554 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DP51 |
#30: Protein | Mass: 6823.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DM33 |
#31: Protein | Mass: 12316.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2E6Z9 |
#40: Protein | Mass: 6297.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2D9N4 |
#42: Protein | Mass: 12471.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DAI6 |
-Protein , 1 types, 1 molecules m
#41: Protein | Mass: 15101.515 Da / Num. of mol.: 1 / Fragment: UNP residues 35-166 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DGL5 |
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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
Component | Name: Large subunit of Trichomonas vaginalis ribosome / Type: RIBOSOME / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Trichomonas vaginalis (eukaryote) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57162 / Symmetry type: POINT |