+Open data
-Basic information
Entry | Database: PDB / ID: 8br8 | ||||||||||||||||||||||||
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Title | Giardia ribosome in POST-T state (A1) | ||||||||||||||||||||||||
Components |
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Keywords | RIBOSOME / Translation / Giardia / Eukaryote / Eukaryotic / Macromolecule / tRNA | ||||||||||||||||||||||||
Function / homology | Function and homology information 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) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway ...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) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / 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 / ribonucleoprotein complex / translation / 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: 3.35 Å | ||||||||||||||||||||||||
Authors | Majumdar, S. / Emmerich, A.G. / Sanyal, S. | ||||||||||||||||||||||||
Funding support | Sweden, United States, 7items
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Citation | Journal: Nucleic Acids Res / Year: 2023 Title: Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis. Authors: Soneya Majumdar / Andrew Emmerich / Sascha Krakovka / Chandra Sekhar Mandava / Staffan G Svärd / Suparna Sanyal / Abstract: Giardia intestinalis is a protozoan parasite that causes diarrhea in humans. Using single-particle cryo-electron microscopy, we have determined high-resolution structures of six naturally populated ...Giardia intestinalis is a protozoan parasite that causes diarrhea in humans. Using single-particle cryo-electron microscopy, we have determined high-resolution structures of six naturally populated translocation intermediates, from ribosomes isolated directly from actively growing Giardia cells. The highly compact and uniquely GC-rich Giardia ribosomes possess eukaryotic rRNAs and ribosomal proteins, but retain some bacterial features. The translocation intermediates, with naturally bound tRNAs and eukaryotic elongation factor 2 (eEF2), display characteristic ribosomal intersubunit rotation and small subunit's head swiveling-universal for translocation. In addition, we observe the eukaryote-specific 'subunit rolling' dynamics, albeit with limited features. Finally, the eEF2·GDP state features a uniquely positioned 'leaving phosphate (Pi)' that proposes hitherto unknown molecular events of Pi and eEF2 release from the ribosome at the final stage of translocation. In summary, our study elucidates the mechanism of translocation in the protists and illustrates evolution of the translation machinery from bacteria to eukaryotes from both the structural and mechanistic perspectives. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8br8.cif.gz | 3.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8br8.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8br8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8br8_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 8br8_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 8br8_validation.xml.gz | 290.1 KB | Display | |
Data in CIF | 8br8_validation.cif.gz | 501.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/8br8 ftp://data.pdbj.org/pub/pdb/validation_reports/br/8br8 | HTTPS FTP |
-Related structure data
Related structure data | 16211MC 8brmC 8bsiC 8bsjC 8btdC 8btrC 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 ... , 52 types, 52 molecules LALBLCLFLGLHLJLKLLLNLOLPLQLRLSLULWLXLYLZLbLdLeLfLgLhLiLjLkLn...
-RNA chain , 5 types, 5 molecules LDLELtLuSt
#4: RNA chain | Mass: 45891.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) |
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#5: RNA chain | Mass: 38993.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) |
#44: RNA chain | Mass: 874762.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) |
#45: RNA chain | Mass: 24231.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) |
#76: RNA chain | Mass: 471227.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) |
-60S ribosomal protein ... , 6 types, 6 molecules LILMLTLaLcLo
#9: Protein | Mass: 25427.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / 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) / 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) / References: UniProt: A8BT04 |
#27: Protein | Mass: 15374.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / References: UniProt: A8B1T3 |
#29: Protein | Mass: 7363.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / References: UniProt: A8BYY2 |
#40: Protein/peptide | Mass: 3283.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / References: UniProt: V6TX21 |
-Protein , 3 types, 3 molecules LVLlLs
#22: Protein | Mass: 14427.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / References: UniProt: A0A644FC41 |
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#38: Protein | Mass: 8605.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / References: UniProt: A8B481 |
#43: Protein | Mass: 14343.675 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / References: UniProt: A8BXE1 |
-40S ribosomal protein ... , 10 types, 10 molecules SASDSESGSHSISYScSdSj
#46: Protein | Mass: 28101.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / References: UniProt: A8BE86 |
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#49: Protein | Mass: 28413.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / References: UniProt: A8BS79 |
#50: Protein | Mass: 30464.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / References: UniProt: A8BFE3 |
#52: Protein | Mass: 28084.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / References: UniProt: A8B6L8 |
#53: Protein | Mass: 21786.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / References: UniProt: A8BT38 |
#54: Protein | Mass: 19451.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / References: UniProt: A8B252 |
#68: Protein | Mass: 9686.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / References: UniProt: A8B484 |
#70: Protein | Mass: 10121.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / References: UniProt: A8B8H7 |
#71: Protein | Mass: 12791.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / References: UniProt: A8BQZ7 |
#75: Protein | Mass: 7932.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Giardia lamblia ATCC 50803 (eukaryote) / References: UniProt: A0A644F843 |
-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 ribosome in POST-T state (A1) / Type: RIBOSOME / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
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 | 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: OTHER |
Electron lens | Mode: OTHER / Nominal defocus max: 1900 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Particle selection | Num. of particles selected: 383193 |
3D reconstruction | Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29181 / Symmetry type: POINT |