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Yorodumi- EMDB-8123: Structure of the Kluyveromyces lactis 80S ribosome in complex wit... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8123 | |||||||||
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Title | Structure of the Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis virus IRES and eEF2 | |||||||||
Map data | None | |||||||||
Sample | eEF2 != Kluyveromyces lactis 80S ribosome in complex with the cricket paralysis virus IRES and eEF2 eEF2
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Function / homology | Function and homology information response to cycloheximide / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / 90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly ...response to cycloheximide / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / 90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / 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) / maturation of LSU-rRNA / cytosolic ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / ribosomal large subunit biogenesis / 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 / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / positive regulation of protein phosphorylation / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Kluyveromyces lactis (yeast) / Cricket paralysis virus / Saccharomyces cerevisiae P283 (yeast) / Yeast (yeast) / Baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Murray J / Savva CG / Shin BS / Dever TE / Ramakrishnan V / Fernandez IS | |||||||||
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_8123.map.gz | 117 MB | EMDB map data format | |
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Header (meta data) | emd-8123-v30.xml emd-8123.xml | 110.6 KB 110.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8123_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_8123.png | 141.1 KB | ||
Masks | emd_8123_msk_1.map emd_8123_msk_2.map | 125 MB 125 MB | Mask map | |
Others | emd_8123_additional_1.map.gz emd_8123_additional_2.map.gz emd_8123_half_map_1.map.gz emd_8123_half_map_2.map.gz | 20.3 MB 97.2 MB 98 MB 98.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8123 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8123 | HTTPS FTP |
-Validation report
Summary document | emd_8123_validation.pdf.gz | 572.3 KB | Display | EMDB validaton report |
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Full document | emd_8123_full_validation.pdf.gz | 571.5 KB | Display | |
Data in XML | emd_8123_validation.xml.gz | 17.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8123 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8123 | HTTPS FTP |
-Related structure data
Related structure data | 5it7MC 8124C 5it9C 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_8123.map.gz / Format: CCP4 / Size: 125 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_8123_msk_1.map | ||||||||||||
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-Mask #2
File | emd_8123_msk_2.map | ||||||||||||
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-Additional map: None
File | emd_8123_additional_1.map | ||||||||||||
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Annotation | None | ||||||||||||
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-Additional map: None
File | emd_8123_additional_2.map | ||||||||||||
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Annotation | None | ||||||||||||
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-Half map: None
File | emd_8123_half_map_1.map | ||||||||||||
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Annotation | None | ||||||||||||
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-Half map: None
File | emd_8123_half_map_2.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : eEF2
+Supramolecule #1: Kluyveromyces lactis 80S ribosome in complex with the cricket par...
+Supramolecule #2: Kluyveromyces lactis 80S ribosome
+Supramolecule #3: Cricket paralysis virus IRES
+Supramolecule #4: eEF2
+Macromolecule #1: 25S ribosomal RNA
+Macromolecule #82: cricket paralysis virus IRES
+Macromolecule #2: 5S ribosomal RNA
+Macromolecule #3: 5.8S ribosomal RNA
+Macromolecule #81: 18S ribosomal RNA
+Macromolecule #4: KLLA0D16027p
+Macromolecule #5: 60S ribosomal protein L3
+Macromolecule #6: KLLA0B07139p
+Macromolecule #7: KLLA0D06941p
+Macromolecule #8: KLLA0B04686p
+Macromolecule #9: KLLA0D03410p
+Macromolecule #10: KLLA0E00573p
+Macromolecule #11: KLLA0F04499p
+Macromolecule #12: KLLA0D05643p
+Macromolecule #13: KLLA0F08261p
+Macromolecule #14: 60S ribosomal protein L13
+Macromolecule #15: KLLA0B13409p
+Macromolecule #16: Ribosomal protein L15
+Macromolecule #17: KLLA0F04675p
+Macromolecule #18: KLLA0A06336p
+Macromolecule #19: KLLA0A07227p
+Macromolecule #20: KLLA0E12453p
+Macromolecule #21: 60S ribosomal protein L20
+Macromolecule #22: KLLA0E23651p
+Macromolecule #23: KLLA0D05181p
+Macromolecule #24: KLLA0E06997p
+Macromolecule #25: 60S ribosomal protein L24
+Macromolecule #26: 60S ribosomal protein L25
+Macromolecule #27: KLLA0B05742p
+Macromolecule #28: KLLA0E03455p
+Macromolecule #29: RPL28
+Macromolecule #30: KLLA0D16071p
+Macromolecule #31: 60S ribosomal protein L30
+Macromolecule #32: KLLA0B02937p
+Macromolecule #33: KLLA0E06843p
+Macromolecule #34: KLLA0D07405p
+Macromolecule #35: KLLA0C08371p
+Macromolecule #36: KLLA0F05247p
+Macromolecule #37: 60S ribosomal protein L36
+Macromolecule #38: Ribosomal protein L37
+Macromolecule #39: KLLA0C18216p
+Macromolecule #40: 60S ribosomal protein L39
+Macromolecule #41: Ubiquitin fusion protein
+Macromolecule #42: 60S ribosomal protein L41-A
+Macromolecule #43: 60S ribosomal protein L44
+Macromolecule #44: KLLA0E05941p
+Macromolecule #45: Ribosomal protein
+Macromolecule #46: 60S acidic ribosomal protein P0
+Macromolecule #47: uL11
+Macromolecule #48: 40S ribosomal protein S0
+Macromolecule #49: 40S ribosomal protein S1
+Macromolecule #50: KLLA0F09812p
+Macromolecule #51: KLLA0D08305p
+Macromolecule #52: 40S ribosomal protein S4
+Macromolecule #53: KLLA0D10659p
+Macromolecule #54: 40S ribosomal protein S6
+Macromolecule #55: KLLA0C13519p
+Macromolecule #56: 40S ribosomal protein S8
+Macromolecule #57: KLLA0E23673p
+Macromolecule #58: KLLA0B08173p
+Macromolecule #59: KLLA0A10483p
+Macromolecule #60: 40S ribosomal protein S12
+Macromolecule #61: KLLA0F18040p
+Macromolecule #62: 40S ribosomal protein S14
+Macromolecule #63: KLLA0F07843p
+Macromolecule #64: 40S ribosomal protein S16
+Macromolecule #65: KLLA0B01474p
+Macromolecule #66: KLLA0B01562p
+Macromolecule #67: KLLA0A07194p
+Macromolecule #68: KLLA0F25542p
+Macromolecule #69: 40S ribosomal protein S21
+Macromolecule #70: 40S ribosomal protein S22
+Macromolecule #71: RPS23
+Macromolecule #72: 40S ribosomal protein S24
+Macromolecule #73: KLLA0B06182p
+Macromolecule #74: KLLA0D05115p
+Macromolecule #75: 40S ribosomal protein S27
+Macromolecule #76: 40S ribosomal protein S28
+Macromolecule #77: 40S ribosomal protein S29
+Macromolecule #78: KLLA0C04809p
+Macromolecule #79: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #80: KLLA0E12277p
+Macromolecule #83: Eft2p
+Macromolecule #84: MAGNESIUM ION
+Macromolecule #85: ZINC ION
+Macromolecule #86: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
+Macromolecule #87: (2S)-1-amino-N,N,N-trimethyl-1-oxobutan-2-aminium
-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 - Concentration: 20.0 millimolar / Component - Name: MES-KOH |
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Vitrification | Cryogen name: ETHANE / 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) / Average electron dose: 30.0 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
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: AB INITIO MODEL |
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Output model | PDB-5it7: |