+Open data
-Basic information
Entry | Database: PDB / ID: 5xyi | ||||||
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Title | Small subunit of Trichomonas vaginalis ribosome | ||||||
Components |
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Keywords | RIBOSOME / Trichomonas vaginalis ribosome / rRNA / rprotein | ||||||
Function / homology | Function and homology information positive regulation of translational fidelity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / mRNA 5'-UTR binding / rRNA processing ...positive regulation of translational fidelity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / mRNA 5'-UTR binding / rRNA processing / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / mRNA binding / nucleolus / enzyme binding / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Trichomonas vaginalis (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 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
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PDBx/mmCIF format | 5xyi.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5xyi.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 5xyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xyi_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5xyi_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5xyi_validation.xml.gz | 126.4 KB | Display | |
Data in CIF | 5xyi_validation.cif.gz | 212.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/5xyi ftp://data.pdbj.org/pub/pdb/validation_reports/xy/5xyi | HTTPS FTP |
-Related structure data
Related structure data | 6788MC 6778C 6780C 6784C 5xxbC 5xxuC 5xy3C 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
-40S ribosomal protein ... , 15 types, 15 molecules AEFGHINQRVXabde
#2: Protein | Mass: 28584.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2EFE7 |
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#6: Protein | Mass: 28589.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2FC75 |
#7: Protein | Mass: 21672.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2E4S6 |
#8: Protein | Mass: 24583.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DEJ9 |
#9: Protein | Mass: 18708.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2G5X6 |
#10: Protein | Mass: 22118.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2E1L5 |
#15: Protein | Mass: 17071.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2D9L2 |
#18: Protein | Mass: 15626.175 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2D919 |
#19: Protein | Mass: 14964.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DPS3 |
#23: Protein | Mass: 9853.130 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2FFS8 |
#25: Protein | Mass: 15592.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2D895 |
#28: Protein | Mass: 13889.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DST7 |
#29: Protein | Mass: 9467.907 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2FBZ2 |
#31: Protein | Mass: 6843.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DYA8 |
#32: Protein | Mass: 6919.079 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2FHY5 |
-Ribosomal protein ... , 10 types, 10 molecules BDMOPSTUWY
#3: Protein | Mass: 28085.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2G9Z8 |
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#5: Protein | Mass: 24505.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DIM3 |
#14: Protein | Mass: 13714.954 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2FA40 |
#16: Protein | Mass: 16689.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: Q76KS8 |
#17: Protein | Mass: 16286.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DVD8 |
#20: Protein | Mass: 17564.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DTR8 |
#21: Protein | Mass: 16584.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2EG54 |
#22: Protein | Mass: 13933.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2FDE0 |
#24: Protein | Mass: 14583.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DLW4 |
#26: Protein | Mass: 16069.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2F0H5 |
-Uncharacterized ... , 5 types, 5 molecules CJLZc
#4: Protein | Mass: 30083.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2EHK3 |
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#11: Protein | Mass: 21811.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DNY3 |
#13: Protein | Mass: 18015.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DHU8 |
#27: Protein | Mass: 12645.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2ER97 |
#30: Protein | Mass: 7650.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2DQN8 |
-Protein , 2 types, 2 molecules Kg
#12: Protein | Mass: 16251.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2EBA2 |
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#33: Protein | Mass: 37151.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: A2ELV7 |
-RNA chain / Protein/peptide , 2 types, 2 molecules 2n
#1: RNA chain | Mass: 508656.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) |
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#34: Protein/peptide | Mass: 3354.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichomonas vaginalis (eukaryote) / References: UniProt: P0CX86*PLUS |
-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: Small 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: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57162 / Symmetry type: POINT |