+Open data
-Basic information
Entry | Database: PDB / ID: 8fvy | ||||||||||||
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Title | 40S subunit of the Giardia lamblia 80S ribosome | ||||||||||||
Components |
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Keywords | RIBOSOME / Giardia lamblia / Ribosome structure / Translation / 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 SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / maintenance of translational fidelity / rRNA processing / ribosomal small subunit biogenesis / ribosomal small subunit assembly ...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 SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / maintenance of translational fidelity / rRNA processing / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleus / cytosol Similarity search - Function | ||||||||||||
Biological species | Giardia intestinalis assemblage A (eukaryote) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å | ||||||||||||
Authors | Eiler, D.R. / Wimberly, B.T. / Bilodeau, D.Y. / Rissland, O.S. / Kieft, J.S. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Structure / Year: 2024 Title: The Giardia lamblia ribosome structure reveals divergence in several biological pathways and the mode of emetine function. Authors: Daniel R Eiler / Brian T Wimberly / Danielle Y Bilodeau / J Matthew Taliaferro / Philip Reigan / Olivia S Rissland / Jeffrey S Kieft / Abstract: Giardia lamblia is a deeply branching protist and a human pathogen. Its unusual biology presents the opportunity to explore conserved and fundamental molecular mechanisms. We determined the structure ...Giardia lamblia is a deeply branching protist and a human pathogen. Its unusual biology presents the opportunity to explore conserved and fundamental molecular mechanisms. We determined the structure of the G. lamblia 80S ribosome bound to tRNA, mRNA, and the antibiotic emetine by cryo-electron microscopy, to an overall resolution of 2.49 Å. The structure reveals rapidly evolving protein and nucleotide regions, differences in the peptide exit tunnel, and likely altered ribosome quality control pathways. Examination of translation initiation factor binding sites suggests these interactions are conserved despite a divergent initiation mechanism. Highlighting the potential of G. lamblia to resolve conserved biological principles; our structure reveals the interactions of the translation inhibitor emetine with the ribosome and mRNA, thus providing insight into the mechanism of action for this widely used antibiotic. Our work defines key questions in G. lamblia and motivates future experiments to explore the diversity of eukaryotic gene regulation. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fvy.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8fvy.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8fvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fvy_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 8fvy_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 8fvy_validation.xml.gz | 140.7 KB | Display | |
Data in CIF | 8fvy_validation.cif.gz | 246.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/8fvy ftp://data.pdbj.org/pub/pdb/validation_reports/fv/8fvy | HTTPS FTP |
-Related structure data
Related structure data | 29495MC 8fruC 8g4sC 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 , 2 types, 2 molecules 2g
#1: RNA chain | Mass: 470516.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: GenBank: 2333213660 |
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#32: RNA chain | Mass: 23749.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) |
-40S ribosomal protein ... , 10 types, 10 molecules ABEGHIVZae
#2: Protein | Mass: 28101.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8BE86 |
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#3: Protein | Mass: 28413.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8BS79 |
#6: Protein | Mass: 30464.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8BFE3 |
#8: Protein | Mass: 28084.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8B6L8 |
#9: Protein | Mass: 23072.963 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: V6TBA3 |
#10: Protein | Mass: 19451.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8B252 |
#22: Protein | Mass: 9686.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8B484 |
#26: Protein | Mass: 10121.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8B8H7 |
#27: Protein | Mass: 12791.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8BQZ7 |
#34: Protein | Mass: 7932.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A0A644F843 |
-Ribosomal protein ... , 17 types, 17 molecules CDJKNOPQRSUYbcdfM
#4: Protein | Mass: 26765.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8BMZ1 |
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#5: Protein | Mass: 24779.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8B8Z2 |
#11: Protein | Mass: 21699.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8BKS8 |
#12: Protein | Mass: 15406.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8BRX3 |
#14: Protein | Mass: 17627.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8BE02 |
#15: Protein | Mass: 15755.995 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: E2RU83 |
#16: Protein | Mass: 16728.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8BBP3 |
#17: Protein | Mass: 17634.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8BKC6 |
#18: Protein | Mass: 15757.351 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8BRG5 |
#19: Protein | Mass: 17510.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8BZ58 |
#21: Protein | Mass: 14073.192 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8B4G0 |
#25: Protein | Mass: 14872.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8B593 |
#28: Protein | Mass: 14117.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8BJL1 |
#29: Protein | Mass: 7358.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8B4F3 |
#30: Protein | Mass: 15499.780 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8B7H6 |
#31: Protein | Mass: 15134.745 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8BNY1 |
#33: Protein | Mass: 14378.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: A8BUG8 |
-SSU ribosomal protein ... , 5 types, 5 molecules FLTWX
#7: Protein | Mass: 21058.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: V6T8P6 |
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#13: Protein | Mass: 23160.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: V6TF82 |
#20: Protein | Mass: 17816.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: V6TE85 |
#23: Protein | Mass: 14770.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: V6TFI0 |
#24: Protein | Mass: 15897.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Giardia intestinalis assemblage A (eukaryote) References: UniProt: V6T9I6 |
-Non-polymers , 4 types, 768 molecules
#35: Chemical | ChemComp-MG / #36: Chemical | ChemComp-YAT / | #37: Chemical | ChemComp-ZN / | #38: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 60S ribosomal subunit of the 80S Giardia intestinalis assemblage A ribosome Type: RIBOSOME / Entity ID: #1-#34 / Source: NATURAL |
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Source (natural) | Organism: Giardia intestinalis assemblage A (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: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1900 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 72.26 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 289618 / Symmetry type: POINT | ||||||||||||||||||||||||
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