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Yorodumi- EMDB-8149: Cryo-EM structure of a full archaeal ribosomal translation initia... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8149 | |||||||||
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Title | Cryo-EM structure of a full archaeal ribosomal translation initiation complex in the P-INconformation | |||||||||
Map data | None | |||||||||
Sample |
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Keywords | transcription | |||||||||
Function / homology | Function and homology information translation reinitiation / protein-synthesizing GTPase / formation of translation preinitiation complex / ribonuclease P activity / tRNA 5'-leader removal / translation elongation factor activity / translation initiation factor activity / translational initiation / ribosomal small subunit biogenesis / ribosome biogenesis ...translation reinitiation / protein-synthesizing GTPase / formation of translation preinitiation complex / ribonuclease P activity / tRNA 5'-leader removal / translation elongation factor activity / translation initiation factor activity / translational initiation / ribosomal small subunit biogenesis / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / GTP binding / RNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Pyrococcus abyssi GE5 (archaea) / Escherichia coli (E. coli) / Pyrococcus (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.34 Å | |||||||||
Authors | COUREUX P-D / SCHMITT E | |||||||||
Citation | Journal: Nat Commun / Year: 2016 Title: Cryo-EM study of start codon selection during archaeal translation initiation. Authors: Pierre-Damien Coureux / Christine Lazennec-Schurdevin / Auriane Monestier / Eric Larquet / Lionel Cladière / Bruno P Klaholz / Emmanuelle Schmitt / Yves Mechulam / Abstract: Eukaryotic and archaeal translation initiation complexes have a common structural core comprising e/aIF1, e/aIF1A, the ternary complex (TC, e/aIF2-GTP-Met-tRNA) and mRNA bound to the small ribosomal ...Eukaryotic and archaeal translation initiation complexes have a common structural core comprising e/aIF1, e/aIF1A, the ternary complex (TC, e/aIF2-GTP-Met-tRNA) and mRNA bound to the small ribosomal subunit. e/aIF2 plays a crucial role in this process but how this factor controls start codon selection remains unclear. Here, we present cryo-EM structures of the full archaeal 30S initiation complex showing two conformational states of the TC. In the first state, the TC is bound to the ribosome in a relaxed conformation with the tRNA oriented out of the P site. In the second state, the tRNA is accommodated within the peptidyl (P) site and the TC becomes constrained. This constraint is compensated by codon/anticodon base pairing, whereas in the absence of a start codon, aIF2 contributes to swing out the tRNA. This spring force concept highlights a mechanism of codon/anticodon probing by the initiator tRNA directly assisted by aIF2. | |||||||||
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_8149.map.gz | 153.1 MB | EMDB map data format | |
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Header (meta data) | emd-8149-v30.xml emd-8149.xml | 53.8 KB 53.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8149_fsc.xml | 11.9 KB | Display | FSC data file |
Images | emd_8149.png | 124.6 KB | ||
Filedesc metadata | emd-8149.cif.gz | 11.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8149 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8149 | HTTPS FTP |
-Validation report
Summary document | emd_8149_validation.pdf.gz | 411.5 KB | Display | EMDB validaton report |
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Full document | emd_8149_full_validation.pdf.gz | 411 KB | Display | |
Data in XML | emd_8149_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | emd_8149_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8149 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8149 | HTTPS FTP |
-Related structure data
Related structure data | 5jbhMC 8148C 5jb3C 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_8149.map.gz / Format: CCP4 / Size: 160.8 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: 1.12 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 : 30S archaeal translation initiation complex
+Supramolecule #1: 30S archaeal translation initiation complex
+Supramolecule #2: 30S archaeal translation initiation complex
+Supramolecule #3: 30S archaeal translation initiation complex
+Supramolecule #4: 30S archaeal translation initiation complex
+Supramolecule #5: 30S archaeal translation initiation complex
+Macromolecule #1: 16S ribosomal RNA
+Macromolecule #30: mRNA
+Macromolecule #32: initiator Met-tRNA fMet from E. coli (A1U72 variant)
+Macromolecule #2: 30S ribosomal protein uS3
+Macromolecule #3: 50S ribosomal protein uL30
+Macromolecule #4: 30S ribosomal protein uS10
+Macromolecule #5: 30S ribosomal protein uS13
+Macromolecule #6: 30S ribosomal protein uS14
+Macromolecule #7: 30S ribosomal protein eS17
+Macromolecule #8: 30S ribosomal protein uS19
+Macromolecule #9: 30S ribosomal protein eS19
+Macromolecule #10: 30S ribosomal protein eS28
+Macromolecule #11: 30S ribosomal protein eS27
+Macromolecule #12: 30S ribosomal protein uS7
+Macromolecule #13: 30S ribosomal protein uS9
+Macromolecule #14: 30S ribosomal protein uS11
+Macromolecule #15: 30S ribosomal protein uS12
+Macromolecule #16: 30S ribosomal protein uS15
+Macromolecule #17: 30S ribosomal protein uS17
+Macromolecule #18: 30S ribosomal protein uS3
+Macromolecule #19: 30S ribosomal protein uS2
+Macromolecule #20: 30S ribosomal protein eS24
+Macromolecule #21: 30S ribosomal protein eS27
+Macromolecule #22: 30S ribosomal protein uS4
+Macromolecule #23: 30S ribosomal protein eS4
+Macromolecule #24: 30S ribosomal protein uS5
+Macromolecule #25: 30S ribosomal protein eS6
+Macromolecule #26: 30S ribosomal protein uS8
+Macromolecule #27: 30S ribosomal protein eS8
+Macromolecule #28: 30S ribosomal protein SX
+Macromolecule #29: 30S ribosomal protein eL41
+Macromolecule #31: aIF1
+Macromolecule #33: aIF1A
+Macromolecule #34: aIF2-gamma
+Macromolecule #35: aIF2-beta
+Macromolecule #36: aIF2-alpha
+Macromolecule #37: METHIONINE
+Macromolecule #38: MAGNESIUM ION
+Macromolecule #39: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
+Macromolecule #40: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-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: 44.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |