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Yorodumi- EMDB-8124: Structure of the yeast Kluyveromyces lactis small ribosomal subun... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8124 | ||||||||||||
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Title | Structure of the yeast Kluyveromyces lactis small ribosomal subunit in complex with the cricket paralysis virus IRES. | ||||||||||||
Map data | None | ||||||||||||
Sample |
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Keywords | IRES / ribosome / small / subunit | ||||||||||||
Function / homology | Function and homology information 90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / 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) / rescue of stalled ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / positive regulation of apoptotic signaling pathway ...90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation regulator activity / 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) / rescue of stalled ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / positive regulation of apoptotic signaling pathway / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / positive regulation of protein phosphorylation / translation / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Kluyveromyces lacti (yeast) / Kluyveromyces lactis (yeast) / Cricket paralysis virus | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Murray J / Savva CG | ||||||||||||
Funding support | United Kingdom, United States, 3 items
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Citation | Journal: Elife / Year: 2016 Title: Structural characterization of ribosome recruitment and translocation by type IV IRES. Authors: Jason Murray / Christos G Savva / Byung-Sik Shin / Thomas E Dever / V Ramakrishnan / Israel S Fernández / Abstract: Viral mRNA sequences with a type IV IRES are able to initiate translation without any host initiation factors. Initial recruitment of the small ribosomal subunit as well as two translocation steps ...Viral mRNA sequences with a type IV IRES are able to initiate translation without any host initiation factors. Initial recruitment of the small ribosomal subunit as well as two translocation steps before the first peptidyl transfer are essential for the initiation of translation by these mRNAs. Using electron cryomicroscopy (cryo-EM) we have structurally characterized at high resolution how the Cricket Paralysis Virus Internal Ribosomal Entry Site (CrPV-IRES) binds the small ribosomal subunit (40S) and the translocation intermediate stabilized by elongation factor 2 (eEF2). The CrPV-IRES restricts tvhe otherwise flexible 40S head to a conformation compatible with binding the large ribosomal subunit (60S). Once the 60S is recruited, the binary CrPV-IRES/80S complex oscillates between canonical and rotated states (Fernández et al., 2014; Koh et al., 2014), as seen for pre-translocation complexes with tRNAs. Elongation factor eEF2 with a GTP analog stabilizes the ribosome-IRES complex in a rotated state with an extra ~3 degrees of rotation. Key residues in domain IV of eEF2 interact with pseudoknot I (PKI) of the CrPV-IRES stabilizing it in a conformation reminiscent of a hybrid tRNA state. The structure explains how diphthamide, a eukaryotic and archaeal specific post-translational modification of a histidine residue of eEF2, is involved in translocation. | ||||||||||||
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_8124.map.gz | 78.4 MB | EMDB map data format | |
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Header (meta data) | emd-8124-v30.xml emd-8124.xml | 55.6 KB 55.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8124_fsc.xml | 9.8 KB | Display | FSC data file |
Images | emd_8124.png | 139.2 KB | ||
Masks | emd_8124_msk_1.map emd_8124_msk_2.map | 83.7 MB 83.7 MB | Mask map | |
Filedesc metadata | emd-8124.cif.gz | 11.5 KB | ||
Others | emd_8124_additional_1.map.gz emd_8124_additional_2.map.gz emd_8124_half_map_1.map.gz emd_8124_half_map_2.map.gz | 11.2 MB 64.9 MB 65.2 MB 65.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8124 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8124 | HTTPS FTP |
-Validation report
Summary document | emd_8124_validation.pdf.gz | 517 KB | Display | EMDB validaton report |
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Full document | emd_8124_full_validation.pdf.gz | 516.1 KB | Display | |
Data in XML | emd_8124_validation.xml.gz | 15.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8124 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8124 | HTTPS FTP |
-Related structure data
Related structure data | 5it9MC 8123C 5it7C 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_8124.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_8124_msk_1.map | ||||||||||||
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-Mask #2
File | emd_8124_msk_2.map | ||||||||||||
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-Additional map: None
File | emd_8124_additional_1.map | ||||||||||||
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-Additional map: None
File | emd_8124_additional_2.map | ||||||||||||
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Annotation | None | ||||||||||||
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-Half map: None
File | emd_8124_half_map_1.map | ||||||||||||
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Annotation | None | ||||||||||||
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-Half map: None
File | emd_8124_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
+Entire : Kluyveromyces lactis small ribosomal subunit in complex with the ...
+Supramolecule #1: Kluyveromyces lactis small ribosomal subunit in complex with the ...
+Macromolecule #1: Ribosomal protein uS2
+Macromolecule #2: Ribosomal protein eS1
+Macromolecule #3: Ribosomal protein uS5
+Macromolecule #4: Ribosomal protein uS3
+Macromolecule #5: Ribosomal protein eS4
+Macromolecule #6: Ribosomal protein uS7
+Macromolecule #7: Ribosomal protein eS6
+Macromolecule #8: Ribosomal protein eS7
+Macromolecule #9: Ribosomal protein eS8
+Macromolecule #10: Ribosomal protein uS4
+Macromolecule #11: Ribosomal protein eS10
+Macromolecule #12: Ribosomal protein uS17
+Macromolecule #13: Ribosomal protein eS12
+Macromolecule #14: Ribosomal protein uS15
+Macromolecule #15: Ribosomal protein uS14
+Macromolecule #16: Ribosomal protein uS19
+Macromolecule #17: Ribosomal protein uS9
+Macromolecule #18: Ribosomal protein eS17
+Macromolecule #19: Ribosomal protein uS13
+Macromolecule #20: Ribosomal protein eS19
+Macromolecule #21: Ribosomal protein uS10
+Macromolecule #22: Ribosomal protein eS21
+Macromolecule #23: Ribosomal protein uS8
+Macromolecule #24: Ribosomal protein uS21
+Macromolecule #25: Ribosomal protein eS24
+Macromolecule #26: Ribosomal protein eS25
+Macromolecule #27: Ribosomal protein eS26
+Macromolecule #28: Ribosomal protein eS27
+Macromolecule #29: Ribosomal protein eS28
+Macromolecule #30: Ribosomal protein eS29
+Macromolecule #31: Ribosomal protein eS30
+Macromolecule #32: Ribosomal protein eS31
+Macromolecule #33: Ribosomal protein RACK1
+Macromolecule #34: 18S ribosomal RNA
+Macromolecule #35: Cricket paralysis virus IRES RNA
+Macromolecule #36: MAGNESIUM ION
+Macromolecule #37: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.5 Component:
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. | ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: OTHER |
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Output model | PDB-5it9: |