+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20952 | |||||||||
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Title | K.lactis 80S ribosome with p/PE tRNA and eIF5B | |||||||||
Map data | ||||||||||
Sample |
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Keywords | translation / ribosome / initiation / eIF5B | |||||||||
Function / homology | Function and homology information formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / response to cycloheximide / translation regulator activity / translation initiation factor binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation initiation factor activity / cytosolic ribosome ...formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / response to cycloheximide / translation regulator activity / translation initiation factor binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation initiation factor activity / cytosolic ribosome / cytosolic ribosome assembly / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytosolic small ribosomal subunit / ribosome binding / large ribosomal subunit / ribosome biogenesis / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / GTPase activity / GTP binding / RNA binding / zinc ion binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Kluyveromyces lactis (yeast) / Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Fernandez IS / Huang BY | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: Long-range interdomain communications in eIF5B regulate GTP hydrolysis and translation initiation. Authors: Bridget Y Huang / Israel S Fernández / Abstract: Translation initiation controls protein synthesis by regulating the delivery of the first aminoacyl-tRNA to messenger RNAs (mRNAs). In eukaryotes, initiation is sophisticated, requiring dozens of ...Translation initiation controls protein synthesis by regulating the delivery of the first aminoacyl-tRNA to messenger RNAs (mRNAs). In eukaryotes, initiation is sophisticated, requiring dozens of protein factors and 2 GTP-regulated steps. The GTPase eIF5B gates progression to elongation during the second GTP-regulated step. Using electron cryomicroscopy (cryo-EM), we imaged an in vitro initiation reaction which is set up with purified yeast components and designed to stall with eIF5B and a nonhydrolyzable GTP analog. A high-resolution reconstruction of a "dead-end" intermediate at 3.6 Å allowed us to visualize eIF5B in its ribosome-bound conformation. We identified a stretch of residues in eIF5B, located close to the γ-phosphate of GTP and centered around the universally conserved tyrosine 837 ( numbering), that contacts the catalytic histidine of eIF5B (H480). Site-directed mutagenesis confirmed the essential role that these residues play in regulating ribosome binding, GTP hydrolysis, and translation initiation both in vitro and in vivo. Our results illustrate how eIF5B transmits the presence of a properly delivered initiator aminoacyl-tRNA at the P site to the distant GTPase center through interdomain communications and underscore the importance of the multidomain architecture in translation factors to sense and communicate ribosomal states. | |||||||||
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_20952.map.gz | 227.7 MB | EMDB map data format | |
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Header (meta data) | emd-20952-v30.xml emd-20952.xml | 100.1 KB 100.1 KB | Display Display | EMDB header |
Images | emd_20952.png | 165.1 KB | ||
Filedesc metadata | emd-20952.cif.gz | 19.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20952 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20952 | HTTPS FTP |
-Related structure data
Related structure data | 6uz7MC 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_20952.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Kluyveromyces lactis 80S ribosome in complex with eIF5B
+Supramolecule #1: Kluyveromyces lactis 80S ribosome in complex with eIF5B
+Macromolecule #1: 25S ribosomal RNA
+Macromolecule #2: RNA (121-MER)
+Macromolecule #3: 5.8S ribosomal RNA
+Macromolecule #81: 18S ribosomal RNA
+Macromolecule #83: RNA (76-MER)
+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: 60S ribosomal protein L29
+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
+Macromolecule #43: 60S ribosomal protein L44
+Macromolecule #44: KLLA0E05941p
+Macromolecule #45: Ribosomal protein
+Macromolecule #46: 60S acidic ribosomal protein P0
+Macromolecule #47: GDPCP
+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: 40S ribosomal protein S7
+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: 40S ribosomal protein S25
+Macromolecule #74: 40S ribosomal protein S26
+Macromolecule #75: 40S ribosomal protein S27
+Macromolecule #76: 40S ribosomal protein S28
+Macromolecule #77: 40S ribosomal protein S29
+Macromolecule #78: 40S ribosomal protein S30
+Macromolecule #79: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #80: KLLA0E12277p
+Macromolecule #82: KLLA0F23265p
+Macromolecule #84: ZINC ION
+Macromolecule #85: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6 |
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Grid | Model: Quantifoil R2/2 / Material: GOLD / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 64815 |
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Startup model | Type of model: EMDB MAP |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 29712 |