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- EMDB-10320: IC2A cryo-EM map of a full archaeal ribosomal translation initiat... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10320 | |||||||||
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Title | IC2A cryo-EM map of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi | |||||||||
![]() | Pab IC2A map | |||||||||
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![]() | Translation initiation / cryo-EM / ribosome / tRNA / evolution / archaea / rRNA modifications | |||||||||
Function / homology | ![]() protein-synthesizing GTPase / formation of translation preinitiation complex / ribonuclease P activity / tRNA 5'-leader removal / translation elongation factor activity / 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 / translational initiation ...protein-synthesizing GTPase / formation of translation preinitiation complex / ribonuclease P activity / tRNA 5'-leader removal / translation elongation factor activity / 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 / translational initiation / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / 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 / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
![]() | Coureux P-D / Mechulam Y / Schmitt E | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation. Authors: Pierre-Damien Coureux / Christine Lazennec-Schurdevin / Sophie Bourcier / Yves Mechulam / Emmanuelle Schmitt / ![]() Abstract: Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP: ...Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP:Met-tRNA. Here, we determine the cryo-EM structure of a 30S:mRNA:aIF1A:aIF2:GTP:Met-tRNA complex from Pyrococcus abyssi at 3.2 Å resolution. It highlights archaeal features in ribosomal proteins and rRNA modifications. We find an aS21 protein, at the location of eS21 in eukaryotic ribosomes. Moreover, we identify an N-terminal extension of archaeal eL41 contacting the P site. We characterize 34 N-acetylcytidines distributed throughout 16S rRNA, likely contributing to hyperthermostability. Without aIF1, the 30S head is stabilized and initiator tRNA is tightly bound to the P site. A network of interactions involving tRNA, mRNA, rRNA modified nucleotides and C-terminal tails of uS9, uS13 and uS19 is observed. Universal features and domain-specific idiosyncrasies of translation initiation are discussed in light of ribosomal structures from representatives of each domain of life. | |||||||||
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 | ![]() | 126.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 61.1 KB 61.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16 KB | Display | ![]() |
Images | ![]() | 129.1 KB | ||
Filedesc metadata | ![]() | 11.8 KB | ||
Others | ![]() ![]() ![]() | 13.7 MB 127.1 MB 127.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6sw9MC ![]() 6swcC ![]() 6swdC ![]() 6sweC 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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Pab IC2A map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Pab IC2A postprocessed map
File | emd_10320_additional.map | ||||||||||||
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Annotation | Pab IC2A postprocessed map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Pab IC2A half2 map
File | emd_10320_half_map_1.map | ||||||||||||
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Annotation | Pab IC2A half2 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Pab IC2A half1 map
File | emd_10320_half_map_2.map | ||||||||||||
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Annotation | Pab IC2A half1 map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Archaeal translation initiation complex devoid of aIF1 - IC2A state
+Supramolecule #1: Archaeal translation initiation complex devoid of aIF1 - IC2A state
+Supramolecule #2: Ribosome
+Supramolecule #3: tRNA
+Supramolecule #4: Translation initiation factor 1A
+Supramolecule #5: mRNA
+Supramolecule #6: Translation initiation factor 2 subunits alpha, beta and gamma
+Macromolecule #1: 16S ribosomal RNA
+Macromolecule #30: mRNA
+Macromolecule #31: initiator Met-tRNA fMet from E. coli (A1U72 variant)
+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 2 subunit gamma
+Macromolecule #34: Translation initiation factor 2 subunit beta
+Macromolecule #35: Translation initiation factor 2 subunit alpha
+Macromolecule #36: MAGNESIUM ION
+Macromolecule #37: ZINC ION
+Macromolecule #38: METHIONINE
+Macromolecule #39: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
+Macromolecule #40: 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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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |