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Yorodumi- EMDB-11232: Cryo-EM structure of the highly atypical cytoplasmic ribosome of ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11232 | |||||||||
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Title | Cryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis | |||||||||
Map data | Combined cryo-EM map of E. gracilis 80S ribosome | |||||||||
Sample |
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Keywords | Single particle cryo-EM RNA modifications / RIBOSOME | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.15 Å | |||||||||
Authors | Matzov D / Halfon H | |||||||||
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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11232.map.gz | 31 MB | EMDB map data format | |
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Header (meta data) | emd-11232-v30.xml emd-11232.xml | 113.8 KB 113.8 KB | Display Display | EMDB header |
Images | emd_11232.png | 72.2 KB | ||
Filedesc metadata | emd-11232.cif.gz | 20.6 KB | ||
Others | emd_11232_additional_1.map.gz emd_11232_additional_2.map.gz emd_11232_additional_3.map.gz emd_11232_additional_4.map.gz emd_11232_additional_5.map.gz emd_11232_additional_6.map.gz | 171.8 MB 153.9 MB 157.7 MB 28 MB 17.4 MB 12.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11232 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11232 | HTTPS FTP |
-Validation report
Summary document | emd_11232_validation.pdf.gz | 262.3 KB | Display | EMDB validaton report |
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Full document | emd_11232_full_validation.pdf.gz | 261.5 KB | Display | |
Data in XML | emd_11232_validation.xml.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11232 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11232 | HTTPS FTP |
-Related structure data
Related structure data | 6zj3MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11232.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Combined cryo-EM map of E. gracilis 80S ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #6
File | emd_11232_additional_1.map | ||||||||||||
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Density Histograms |
-Additional map: #1
File | emd_11232_additional_2.map | ||||||||||||
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-Additional map: #2
File | emd_11232_additional_3.map | ||||||||||||
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-Additional map: #3
File | emd_11232_additional_4.map | ||||||||||||
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-Additional map: #4
File | emd_11232_additional_5.map | ||||||||||||
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Density Histograms |
-Additional map: #5
File | emd_11232_additional_6.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Euglena gracilis 80S ribosome
+Supramolecule #1: Euglena gracilis 80S ribosome
+Macromolecule #1: 18S rRNA
+Macromolecule #2: A-tRNA
+Macromolecule #3: P-tRNA
+Macromolecule #4: E-tRNA
+Macromolecule #5: A-site tRNA
+Macromolecule #40: 5.8S rRNA
+Macromolecule #41: LSU rRNA chain 1
+Macromolecule #42: LSU rRNA chain 2
+Macromolecule #43: LSU rRNA chain 3
+Macromolecule #44: LSU rRNA chain 4
+Macromolecule #45: LSU rRNA chain 5
+Macromolecule #46: LSU rRNA chain 6
+Macromolecule #47: LSU rRNA chain 7
+Macromolecule #48: LSU rRNA chain 8
+Macromolecule #49: LSU rRNA chain 9
+Macromolecule #50: LSU rRNA chain 10
+Macromolecule #51: LSU rRNA chain 11
+Macromolecule #52: LSU rRNA chain 12
+Macromolecule #53: LSU rRNA chain 13
+Macromolecule #54: 5S rRNA
+Macromolecule #6: Ribosomal protein eS1
+Macromolecule #7: Ribosomal protein uS2
+Macromolecule #8: Ribosomal protein uS3
+Macromolecule #9: Ribosomal protein uS4
+Macromolecule #10: Ribosomal protein eS4
+Macromolecule #11: Ribosomal protein uS5
+Macromolecule #12: Ribosomal protein eS6
+Macromolecule #13: Ribosomal protein uS7
+Macromolecule #14: Ribosomal protein eS7
+Macromolecule #15: Ribosomal protein uS8
+Macromolecule #16: Ribosomal protein eS8
+Macromolecule #17: Ribosomal protein uS9
+Macromolecule #18: Ribosomal protein uS10
+Macromolecule #19: Ribosomal protein eS10
+Macromolecule #20: Ribosomal protein uS11
+Macromolecule #21: Ribosomal protein uS12
+Macromolecule #22: Ribosomal protein eS12
+Macromolecule #23: Ribosomal protein uS13
+Macromolecule #24: Ribosomal protein uS14
+Macromolecule #25: Ribosomal protein uS15
+Macromolecule #26: Ribosomal protein uS17
+Macromolecule #27: Ribosomal protein eS17
+Macromolecule #28: Ribosomal protein uS19
+Macromolecule #29: Ribosomal protein eS19
+Macromolecule #30: Ribosomal protein eS21
+Macromolecule #31: Ribosomal protein eS24
+Macromolecule #32: Ribosomal protein eS25
+Macromolecule #33: Ribosomal protein eS26
+Macromolecule #34: Ribosomal protein eS27
+Macromolecule #35: Ribosomal protein eS28
+Macromolecule #36: Ribosomal protein eS30
+Macromolecule #37: Ribosomal protein eS31
+Macromolecule #38: Ribosomal protein eSEug1
+Macromolecule #39: RACK1
+Macromolecule #55: Ribosomal protein uL2
+Macromolecule #56: Ribosomal protein uL3
+Macromolecule #57: Ribosomal protein uL4
+Macromolecule #58: Ribosomal protein uL5
+Macromolecule #59: Ribosomal protein uL6
+Macromolecule #60: Ribosomal protein eL6
+Macromolecule #61: 60S ribosomal protein L7a
+Macromolecule #62: Ribosomal protein uL13
+Macromolecule #63: Ribosomal protein eL13
+Macromolecule #64: Ribosomal protein uL14
+Macromolecule #65: Ribosomal protein eL14
+Macromolecule #66: Ribosomal protein uL15
+Macromolecule #67: Ribosomal protein eL15
+Macromolecule #68: 60S ribosomal protein L10
+Macromolecule #69: Ribosomal protein uL18
+Macromolecule #70: Ribosomal protein eL18
+Macromolecule #71: Ribosomal protein eL19
+Macromolecule #72: Ribosomal protein eL20
+Macromolecule #73: Ribosomal protein eL21
+Macromolecule #74: Ribosomal protein uL22
+Macromolecule #75: Ribosomal protein eL22
+Macromolecule #76: Ribosomal protein uL23
+Macromolecule #77: Ribosomal protein uL24
+Macromolecule #78: Ribosomal protein eL24
+Macromolecule #79: Ribosomal protein eL27
+Macromolecule #80: Ribosomal protein eLEgr1
+Macromolecule #81: Ribosomal protein uL29
+Macromolecule #82: Ribosomal protein eL29
+Macromolecule #83: Ribosomal protein uL30
+Macromolecule #84: Ribosomal protein eL30
+Macromolecule #85: Ribosomal protein eL31
+Macromolecule #86: Ribosomal protein eL32
+Macromolecule #87: Ribosomal protein eL33
+Macromolecule #88: Ribosomal protein eL34
+Macromolecule #89: Ribosomal protein eL36
+Macromolecule #90: Ribosomal protein eL37
+Macromolecule #91: Ribosomal protein eL38
+Macromolecule #92: Ribosomal protein eL39
+Macromolecule #93: Ribosomal protein eL40
+Macromolecule #94: Ribosomal protein eL41
+Macromolecule #95: Ribosomal protein eL42
+Macromolecule #96: Ribosomal protein eL43
+Macromolecule #97: Ribosomal protein eLEgr2
+Macromolecule #98: Ribosomal protein eLEgr3
+Macromolecule #99: ZINC ION
+Macromolecule #100: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.52 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | #0 - Type of model: PDB ENTRY #0 - PDB model - PDB ID: #1 - Type of model: PDB ENTRY #1 - PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 176308 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |