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Yorodumi- EMDB-4083: Structure of bacterial 30S-IF1-IF2-IF3-mRNA-tRNA translation pre-... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4083 | |||||||||
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Title | Structure of bacterial 30S-IF1-IF2-IF3-mRNA-tRNA translation pre-initiation complex(state-III) | |||||||||
Map data | For optimal visualization of IF3 N-terminal domain, gauss-filter the map by 1.34 and display it at 0.05 contour | |||||||||
Sample |
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Function / homology | Function and homology information ribosome disassembly / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / translation initiation factor activity / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...ribosome disassembly / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / translation initiation factor activity / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / zinc ion binding / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Thermus thermophilus HB8 (bacteria) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 Å | |||||||||
Authors | Hussain T / Llacer JL / Wimberly BT / Ramakrishnan V | |||||||||
Citation | Journal: Cell / Year: 2016 Title: Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation. Authors: Tanweer Hussain / Jose L Llácer / Brian T Wimberly / Jeffrey S Kieft / V Ramakrishnan / Abstract: In bacterial translational initiation, three initiation factors (IFs 1-3) enable the selection of initiator tRNA and the start codon in the P site of the 30S ribosomal subunit. Here, we report 11 ...In bacterial translational initiation, three initiation factors (IFs 1-3) enable the selection of initiator tRNA and the start codon in the P site of the 30S ribosomal subunit. Here, we report 11 single-particle cryo-electron microscopy (cryoEM) reconstructions of the complex of bacterial 30S subunit with initiator tRNA, mRNA, and IFs 1-3, representing different steps along the initiation pathway. IF1 provides key anchoring points for IF2 and IF3, thereby enhancing their activities. IF2 positions a domain in an extended conformation appropriate for capturing the formylmethionyl moiety charged on tRNA. IF3 and tRNA undergo large conformational changes to facilitate the accommodation of the formylmethionyl-tRNA (fMet-tRNA(fMet)) into the P site for start codon recognition. | |||||||||
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_4083.map.gz | 62.5 MB | EMDB map data format | |
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Header (meta data) | emd-4083-v30.xml emd-4083.xml | 42.8 KB 42.8 KB | Display Display | EMDB header |
Images | emd_4083.png | 184.5 KB | ||
Others | emd_4083_half_map_1.map.gz emd_4083_half_map_2.map.gz | 58.2 MB 58.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4083 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4083 | HTTPS FTP |
-Validation report
Summary document | emd_4083_validation.pdf.gz | 437.4 KB | Display | EMDB validaton report |
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Full document | emd_4083_full_validation.pdf.gz | 436.5 KB | Display | |
Data in XML | emd_4083_validation.xml.gz | 10.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4083 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4083 | HTTPS FTP |
-Related structure data
Related structure data | 5lmvMC 4073C 4074C 4075C 4076C 4077C 4078C 4079C 4080C 4081C 4082C 5lmnC 5lmoC 5lmpC 5lmqC 5lmrC 5lmsC 5lmtC 5lmuC 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_4083.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | For optimal visualization of IF3 N-terminal domain, gauss-filter the map by 1.34 and display it at 0.05 contour | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_4083_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_4083_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 30S-IF1-IF2-IF3-mRNA-tRNA pre-initiation complex (state-III)
+Supramolecule #1: 30S-IF1-IF2-IF3-mRNA-tRNA pre-initiation complex (state-III)
+Macromolecule #1: 16S ribosomal RNA
+Macromolecule #24: mRNA
+Macromolecule #25: tRNAi
+Macromolecule #2: 30S ribosomal protein S2
+Macromolecule #3: 30S ribosomal protein S3
+Macromolecule #4: 30S ribosomal protein S4
+Macromolecule #5: 30S ribosomal protein S5
+Macromolecule #6: 30S ribosomal protein S6
+Macromolecule #7: 30S ribosomal protein S7
+Macromolecule #8: 30S ribosomal protein S8
+Macromolecule #9: 30S ribosomal protein S9
+Macromolecule #10: 30S ribosomal protein S10
+Macromolecule #11: 30S ribosomal protein S11
+Macromolecule #12: 30S ribosomal protein S12
+Macromolecule #13: 30S ribosomal protein S13
+Macromolecule #14: 30S ribosomal protein S14 type Z
+Macromolecule #15: 30S ribosomal protein S15
+Macromolecule #16: 30S ribosomal protein S16
+Macromolecule #17: 30S ribosomal protein S17
+Macromolecule #18: 30S ribosomal protein S18
+Macromolecule #19: 30S ribosomal protein S19
+Macromolecule #20: 30S ribosomal protein S20
+Macromolecule #21: 30S ribosomal protein Thx
+Macromolecule #22: Translation initiation factor IF-1
+Macromolecule #23: Translation initiation factor IF-3
+Macromolecule #26: Translation initiation factor IF-2
+Macromolecule #27: ZINC ION
+Macromolecule #28: MAGNESIUM ION
+Macromolecule #29: N-FORMYLMETHIONINE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.065 mg/mL | ||||||||||||
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Buffer | pH: 6.5 Component:
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 90.0 K / Max: 100.0 K |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Number grids imaged: 1 / Number real images: 3200 / Average exposure time: 1.5 sec. / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 104478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: OTHER / Target criteria: FSC |
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Output model | PDB-5lmv: |