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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20952 | |||||||||
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Title | K.lactis 80S ribosome with p/PE tRNA and eIF5B | |||||||||
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![]() | translation / ribosome / initiation / eIF5B | |||||||||
Function / homology | ![]() formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / response to cycloheximide / 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) / translation initiation factor binding / translation initiation factor activity ...formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / regulation of translational initiation / response to cycloheximide / 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) / translation initiation factor binding / translation initiation factor activity / 90S preribosome / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / ribosomal large subunit biogenesis / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / response to antibiotic / GTPase activity / mRNA binding / ubiquitin protein ligase binding / nucleolus / GTP binding / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Fernandez IS / Huang BY | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 227.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 100.1 KB 100.1 KB | Display Display | ![]() |
Images | ![]() | 165.1 KB | ||
Filedesc metadata | ![]() | 19.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6uz7MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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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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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |