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Yorodumi- PDB-7pwg: Cryo-EM structure of large subunit of Giardia lamblia ribosome at... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pwg | ||||||
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Title | Cryo-EM structure of large subunit of Giardia lamblia ribosome at 2.7 A resolution | ||||||
Components |
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Keywords | RIBOSOME / giardia / parasite | ||||||
Function / homology | Function and homology information 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 / large ribosomal subunit rRNA binding / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit ...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 / 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 / metal ion binding Similarity search - Function | ||||||
Biological species | Giardia lamblia ATCC 50803 (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å | ||||||
Authors | Hiregange, D.G. / Rivalta, A. / Bose, T. / Breiner-Goldstein, E. / Samiya, S. / Cimicata, G. / Kulakova, L. / Zimmerman, E. / Bashan, A. / Herzberg, O. / Yonath, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res / Year: 2022 Title: Cryo-EM structure of the ancient eukaryotic ribosome from the human parasite Giardia lamblia. Authors: Disha-Gajanan Hiregange / Andre Rivalta / Tanaya Bose / Elinor Breiner-Goldstein / Sarit Samiya / Giuseppe Cimicata / Liudmila Kulakova / Ella Zimmerman / Anat Bashan / Osnat Herzberg / Ada Yonath / Abstract: Giardiasis is a disease caused by the protist Giardia lamblia. As no human vaccines have been approved so far against it, and resistance to current drugs is spreading, new strategies for combating ...Giardiasis is a disease caused by the protist Giardia lamblia. As no human vaccines have been approved so far against it, and resistance to current drugs is spreading, new strategies for combating giardiasis need to be developed. The G. lamblia ribosome may provide a promising therapeutic target due to its distinct sequence differences from ribosomes of most eukaryotes and prokaryotes. Here, we report the cryo-electron microscopy structure of the G. lamblia (WB strain) ribosome determined at 2.75 Å resolution. The ribosomal RNA is the shortest known among eukaryotes, and lacks nearly all the eukaryote-specific ribosomal RNA expansion segments. In contrast, the ribosomal proteins are typically eukaryotic with some species-specific insertions/extensions. Most typical inter-subunit bridges are maintained except for one missing contact site. Unique structural features are located mainly at the ribosome's periphery. These may be exploited as target sites for the design of new compounds that inhibit selectively the parasite's ribosomal activity. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pwg.cif.gz | 3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7pwg.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7pwg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pwg_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7pwg_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7pwg_validation.xml.gz | 179.3 KB | Display | |
Data in CIF | 7pwg_validation.cif.gz | 330 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/7pwg ftp://data.pdbj.org/pub/pdb/validation_reports/pw/7pwg | HTTPS FTP |
-Related structure data
Related structure data | 13681MC 7pwfC 7pwoC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 5 types, 5 molecules 134wE
#1: RNA chain | Mass: 878254.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 |
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#2: RNA chain | Mass: 38671.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 |
#3: RNA chain | Mass: 44971.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 |
#42: RNA chain | Mass: 24500.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 |
#44: RNA chain | Mass: 894.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 |
+Ribosomal protein ... , 32 types, 32 molecules ABCDFHIJMNOPQRTUVXYacdefghijlopW
-60S ribosomal protein ... , 5 types, 5 molecules GLSZb
#9: Protein | Mass: 25427.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BLL7 |
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#13: Protein | Mass: 26640.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8B6M8 |
#20: Protein | Mass: 20624.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BT04 |
#26: Protein | Mass: 15374.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8B1T3 |
#28: Protein | Mass: 7363.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BYY2 |
-Protein , 2 types, 2 molecules km
#37: Protein | Mass: 8605.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8B481 |
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#39: Protein | Mass: 14343.675 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / WB clone C6 / References: UniProt: A8BXE1 |
-Non-polymers , 4 types, 4691 molecules
#45: Chemical | ChemComp-MG / #46: Chemical | ChemComp-K / #47: Chemical | ChemComp-PGE / | #48: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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Has protein modification | Y |
-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: Giardia lamblia ribosome / Type: RIBOSOME / Entity ID: #1-#44 / Source: NATURAL |
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Source (natural) | Organism: Giardia intestinalis (strain ATCC 50803 / WB clone C6) (eukaryote) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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 / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91058 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE | ||||||||||||||||||||||||
Refine LS restraints |
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