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Yorodumi- PDB-6zj3: Cryo-EM structure of the highly atypical cytoplasmic ribosome of ... -
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-Basic information
Entry | Database: PDB / ID: 6zj3 | ||||||
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Title | Cryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis | ||||||
Components |
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Keywords | RIBOSOME / Single particle cryo-EM RNA modifications | ||||||
Function / homology | Function and homology information maturation of LSU-rRNA / ribosomal large subunit assembly / cytosolic large ribosomal subunit / structural constituent of ribosome / translation / RNA binding Similarity search - Function | ||||||
Biological species | Euglena gracilis (euglena) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å | ||||||
Authors | Matzov, D. / Halfon, H. / Zimmerman, E. / Rozenberg, H. / Bashan, A. / Gray, M.W. / Yonath, A.E. / Shalev-Benami, M. | ||||||
Citation | Journal: Nucleic Acids Res / Year: 2020 Title: Cryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis. Authors: Donna Matzov / Masato Taoka / Yuko Nobe / Yoshio Yamauchi / Yehuda Halfon / Nofar Asis / Ella Zimermann / Haim Rozenberg / Anat Bashan / Shashi Bhushan / Toshiaki Isobe / Michael W Gray / ...Authors: Donna Matzov / Masato Taoka / Yuko Nobe / Yoshio Yamauchi / Yehuda Halfon / Nofar Asis / Ella Zimermann / Haim Rozenberg / Anat Bashan / Shashi Bhushan / Toshiaki Isobe / Michael W Gray / Ada Yonath / Moran Shalev-Benami / Abstract: Ribosomal RNA is the central component of the ribosome, mediating its functional and architectural properties. Here, we report the cryo-EM structure of a highly divergent cytoplasmic ribosome from ...Ribosomal RNA is the central component of the ribosome, mediating its functional and architectural properties. Here, we report the cryo-EM structure of a highly divergent cytoplasmic ribosome from the single-celled eukaryotic alga Euglena gracilis. The Euglena large ribosomal subunit is distinct in that it contains 14 discrete rRNA fragments that are assembled non-covalently into the canonical ribosome structure. The rRNA is substantially enriched in post-transcriptional modifications that are spread far beyond the catalytic RNA core, contributing to the stabilization of this highly fragmented ribosome species. A unique cluster of five adenosine base methylations is found in an expansion segment adjacent to the protein exit tunnel, such that it is positioned for interaction with the nascent peptide. As well as featuring distinctive rRNA expansion segments, the Euglena ribosome contains four novel ribosomal proteins, localized to the ribosome surface, three of which do not have orthologs in other eukaryotes. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6zj3.cif.gz | 4.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6zj3.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6zj3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zj3_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6zj3_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6zj3_validation.xml.gz | 375.7 KB | Display | |
Data in CIF | 6zj3_validation.cif.gz | 641.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/6zj3 ftp://data.pdbj.org/pub/pdb/validation_reports/zj/6zj3 | HTTPS FTP |
-Related structure data
Related structure data | 11232MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 7 types, 7 molecules S1S2S3S4S5LALO
#1: RNA chain | Mass: 747444.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
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#2: RNA chain | Mass: 24599.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
#3: RNA chain | Mass: 24422.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
#4: RNA chain | Mass: 24509.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
#5: RNA chain | Mass: 3756.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
#40: RNA chain | Mass: 52665.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
#54: RNA chain | Mass: 38652.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
+Ribosomal protein ... , 75 types, 75 molecules SASBSCSDSESFSGSHSISJSKSLSMSNSOSPSQSRSSSTSUSVSWSXSYSZSaSbScSd...
-Protein , 1 types, 1 molecules Sh
#39: Protein | Mass: 34755.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
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-LSU rRNA chain ... , 13 types, 13 molecules LBLCLDLELFLGLHLILJLKLLLMLN
#41: RNA chain | Mass: 42961.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
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#42: RNA chain | Mass: 113512.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
#43: RNA chain | Mass: 37346.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
#44: RNA chain | Mass: 225354.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
#45: RNA chain | Mass: 170807.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
#46: RNA chain | Mass: 75508.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
#47: RNA chain | Mass: 240660.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
#48: RNA chain | Mass: 199055.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
#49: RNA chain | Mass: 52952.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
#50: RNA chain | Mass: 20618.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
#51: RNA chain | Mass: 30874.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
#52: RNA chain | Mass: 18673.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
#53: RNA chain | Mass: 27779.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) |
-60S ribosomal protein ... , 2 types, 2 molecules LVLc
#61: Protein | Mass: 32999.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: Q4VH13 |
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#68: Protein | Mass: 24695.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Euglena gracilis (euglena) / References: UniProt: Q39724 |
-Non-polymers , 2 types, 1199 molecules
#99: Chemical | ChemComp-ZN / #100: 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: Euglena gracilis 80S ribosome / Type: RIBOSOME / Entity ID: #1-#98 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Euglena gracilis (euglena) |
Buffer solution | pH: 7.6 |
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: BRIGHT FIELD |
Image recording | Electron dose: 1.52 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: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176308 / Symmetry type: POINT |