+Open data
-Basic information
Entry | Database: PDB / ID: 7pkq | |||||||||||||||
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Title | Small subunit of the Chlamydomonas reinhardtii mitoribosome | |||||||||||||||
Components |
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Keywords | RIBOSOME / Mitochondria / mitoribosome / alga | |||||||||||||||
Function / homology | Function and homology information mitochondrial small ribosomal subunit / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / small ribosomal subunit / rRNA binding / ribosome / mitochondrial matrix ...mitochondrial small ribosomal subunit / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / small ribosomal subunit / rRNA binding / ribosome / mitochondrial matrix / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / mitochondrion / RNA binding / nucleus / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||||||||
Authors | Waltz, F. / Soufari, H. / Hashem, Y. | |||||||||||||||
Funding support | France, 4items
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Citation | Journal: To Be Published Title: The Chlamydomonas mitochondrial ribosome: how to build a ribosome from RNA fragments Authors: Waltz, F. / Salinas-Giege, T. / Englmeier, R. / Meichel, H. / Soufari, H. / Kuhn, L. / Pfeffer, S. / Foerster, F. / Engel, B.D. / Giege, P. / Drouard, L. / Hashem, Y. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pkq.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7pkq.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 7pkq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/7pkq ftp://data.pdbj.org/pub/pdb/validation_reports/pk/7pkq | HTTPS FTP |
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-Related structure data
Related structure data | 13477MC 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
+Protein , 34 types, 36 molecules BCDKLMNOPVWXYZdprwabeozvqlhkju...
-Protein/peptide , 1 types, 1 molecules U
#8: Protein/peptide | Mass: 2826.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) |
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-Mitochondrial ribosomal protein ... , 3 types, 3 molecules fmn
#15: Protein | Mass: 13661.864 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JGX6 |
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#34: Protein | Mass: 13758.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J3J1 |
#35: Protein | Mass: 13009.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J6P9 |
-RNA chain , 4 types, 4 molecules 1423
#19: RNA chain | Mass: 32590.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: GenBank: 12503 |
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#20: RNA chain | Mass: 133231.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) |
#21: RNA chain | Mass: 68527.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: GenBank: 12503 |
#22: RNA chain | Mass: 126928.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: GenBank: 12503 |
-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 the Chlamydomonas reinhardtii mitochondrial ribosome Type: RIBOSOME / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Chlamydomonas reinhardtii (plant) / Organelle: Mitochondrion |
Buffer solution | pH: 7.6 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40131 / Num. of class averages: 1 / Symmetry type: POINT |