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Yorodumi- PDB-7pwo: Cryo-EM structure of Giardia lamblia ribosome at 2.75 A resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pwo | ||||||
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Title | Cryo-EM structure of Giardia lamblia ribosome at 2.75 A resolution | ||||||
Components |
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Keywords | RIBOSOME / giardia / parasite | ||||||
Function / homology | Function and homology information endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / 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) / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / modification-dependent protein catabolic process ...endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / 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) / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol 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 | 7pwo.cif.gz | 4.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7pwo.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7pwo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pwo_validation.pdf.gz | 802.3 KB | Display | wwPDB validaton report |
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Full document | 7pwo_full_validation.pdf.gz | 932 KB | Display | |
Data in XML | 7pwo_validation.xml.gz | 218.5 KB | Display | |
Data in CIF | 7pwo_validation.cif.gz | 371.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/7pwo ftp://data.pdbj.org/pub/pdb/validation_reports/pw/7pwo | HTTPS FTP |
-Related structure data
Related structure data | 13683MC 7pwfC 7pwgC 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
+Ribosomal protein ... , 51 types, 51 molecules T1N1J1D1X1S1Q1C1b1R1K1n1c1O1W1U1A2B2C2D2F2H2I2J2M2N2O2P2Q2R2...
-40S ribosomal protein ... , 9 types, 9 molecules B1a1V1I1e1H1E1G1A1
#9: Protein | Mass: 28413.148 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: A8BS79 |
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#11: Protein | Mass: 12791.023 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: A8BQZ7 |
#12: Protein | Mass: 9686.149 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: A8B484 |
#15: Protein | Mass: 19451.555 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: A8B252 |
#16: Protein | Mass: 7932.407 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: A0A644F843 |
#17: Protein | Mass: 21786.453 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: A8BT38 |
#22: Protein | Mass: 30464.781 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: A8BFE3 |
#72: Protein | Mass: 28084.123 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: A8B6L8 |
#74: Protein | Mass: 28101.803 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: A8BE86 |
-Protein , 3 types, 3 molecules L1k2m2
#23: Protein | Mass: 23244.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / References: UniProt: V6TVJ7 |
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#61: 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 |
#63: 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 |
-RNA chain , 6 types, 6 molecules 1342w2E2
#25: RNA chain | Mass: 878238.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) |
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#26: RNA chain | Mass: 38671.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) |
#27: RNA chain | Mass: 44971.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / References: GenBank: 9351 |
#66: RNA chain | Mass: 4459.755 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) |
#68: RNA chain | Mass: 894.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) |
#73: RNA chain | Mass: 471124.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) |
-60S ribosomal protein ... , 5 types, 5 molecules G2L2S2Z2b2
#33: 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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#37: 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 |
#44: 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 |
#50: 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 |
#52: 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 |
-Non-polymers , 2 types, 556 molecules
#75: Chemical | ChemComp-K / #76: Chemical | ChemComp-MG / |
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-Details
Has ligand of interest | N |
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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: Giardia lamblia ribosome / Type: RIBOSOME / Entity ID: #1-#74 / Source: NATURAL |
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Source (natural) | Organism: Giardia lamblia ATCC 50803 (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) / Num. of grids imaged: 1 / Num. of real images: 5567 |
-Processing
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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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