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- EMDB-14579: Cryo-EM structure of a Pyrococcus abyssi 30S bound to Met-initiat... -
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Open data
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Basic information
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Title | Cryo-EM structure of a Pyrococcus abyssi 30S bound to Met-initiator tRNA,mRNA, aIF1A and the C-terminal domain of aIF5B. | |||||||||
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![]() | Initiation complex / translation initiation / small ribosomal subunit / aIF5b / TRANSLATION | |||||||||
Function / homology | ![]() intein-mediated protein splicing / intron homing / ribonuclease P activity / tRNA 5'-leader removal / translation initiation factor activity / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosome biogenesis / ribosomal small subunit biogenesis ...intein-mediated protein splicing / intron homing / ribonuclease P activity / tRNA 5'-leader removal / translation initiation factor activity / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / endonuclease activity / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.77 Å | |||||||||
![]() | Coureux PD / Bourgeois G / Mechulam Y / Schmitt E / Kazan R | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Role of aIF5B in archaeal translation initiation. Authors: Ramy Kazan / Gabrielle Bourgeois / Christine Lazennec-Schurdevin / Eric Larquet / Yves Mechulam / Pierre-Damien Coureux / Emmanuelle Schmitt / ![]() Abstract: In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established ...In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established and structural data showing eIF5B bound to the full ribosome were obtained. To achieve its function, eIF5B collaborates with eIF1A. However, structural data illustrating how these two factors interact on the small ribosomal subunit have long been awaited. The role of the archaeal counterparts, aIF5B and aIF1A, remains to be extensively addressed. Here, we study the late steps of Pyrococcus abyssi translation initiation. Using in vitro reconstituted initiation complexes and light scattering, we show that aIF5B bound to GTP accelerates subunit joining without the need for GTP hydrolysis. We report the crystallographic structures of aIF5B bound to GDP and GTP and analyze domain movements associated to these two nucleotide states. Finally, we present the cryo-EM structure of an initiation complex containing 30S bound to mRNA, Met-tRNAiMet, aIF5B and aIF1A at 2.7 Å resolution. Structural data shows how archaeal 5B and 1A factors cooperate to induce a conformation of the initiator tRNA favorable to subunit joining. Archaeal and eukaryotic features of late steps of translation initiation are discussed. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 244.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 55.8 KB 55.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15.3 KB | Display | ![]() |
Images | ![]() | 100 KB | ||
Masks | ![]() | 307.5 MB | ![]() | |
Filedesc metadata | ![]() | 11.6 KB | ||
Others | ![]() ![]() | 245.3 MB 245.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 996.3 KB | Display | ![]() |
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Full document | ![]() | 996 KB | Display | |
Data in XML | ![]() | 22.8 KB | Display | |
Data in CIF | ![]() | 30.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zagMC ![]() 7yypC ![]() 7yznC ![]() 7zahC ![]() 7zaiC ![]() 7zhgC ![]() 7zkiC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 0.86 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #2
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
+Entire : Complex of 30S ribosomal subunit with initiation factor aIF1A, th...
+Supramolecule #1: Complex of 30S ribosomal subunit with initiation factor aIF1A, th...
+Supramolecule #2: 30S and 50S ribosomal proteins
+Supramolecule #3: mRNA
+Supramolecule #4: Met-tRNAiMET, Translation initiation factor 1A and Translation in...
+Macromolecule #1: rRNA
+Macromolecule #30: mRNA
+Macromolecule #31: Met-tRNAiMET
+Macromolecule #2: 30S ribosomal protein S3Ae
+Macromolecule #3: 30S ribosomal protein S2
+Macromolecule #4: Zn-ribbon RNA-binding protein involved in translation
+Macromolecule #5: 30S ribosomal protein S4
+Macromolecule #6: 30S ribosomal protein S4e
+Macromolecule #7: 30S ribosomal protein S5
+Macromolecule #8: 30S ribosomal protein S6e
+Macromolecule #9: 30S ribosomal protein S7
+Macromolecule #10: 30S ribosomal protein S8
+Macromolecule #11: 30S ribosomal protein S8e
+Macromolecule #12: 30S ribosomal protein S9
+Macromolecule #13: 30S ribosomal protein S10
+Macromolecule #14: 30S ribosomal protein S11
+Macromolecule #15: 30S ribosomal protein S12
+Macromolecule #16: 30S ribosomal protein S13
+Macromolecule #17: 30S ribosomal protein S14 type Z
+Macromolecule #18: 30S ribosomal protein S15
+Macromolecule #19: 30S ribosomal protein S17
+Macromolecule #20: 30S ribosomal protein S17e
+Macromolecule #21: 30S ribosomal protein S19
+Macromolecule #22: 30S ribosomal protein S19e
+Macromolecule #23: 30S ribosomal protein S24e
+Macromolecule #24: 30S ribosomal protein S27e
+Macromolecule #25: 30S ribosomal protein S28e
+Macromolecule #26: 30S ribosomal protein S27ae
+Macromolecule #27: 30S ribosomal protein S3
+Macromolecule #28: 50S ribosomal protein L41e
+Macromolecule #29: 50S ribosomal protein L7Ae
+Macromolecule #32: Translation initiation factor 1A
+Macromolecule #33: Translation initiation factor 5B
+Macromolecule #34: MAGNESIUM ION
+Macromolecule #35: ZINC ION
+Macromolecule #36: METHIONINE
+Macromolecule #37: water
-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: 6.7 |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 39.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |