+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0662 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | 70S initiation complex | |||||||||||||||
Map data | 70S initiation complex with IF2 and P/I tRNA | |||||||||||||||
Sample |
| |||||||||||||||
Function / homology | Function and homology information guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / ribosomal small subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity ...guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / ribosomal small subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / four-way junction DNA binding / translational termination / DnaA-L2 complex / chaperone-mediated protein folding / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / translation initiation factor activity / response to cold / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / transcription antitermination / response to reactive oxygen species / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / negative regulation of DNA-templated transcription / GTPase activity / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||||||||
Authors | Frank J / Gonzalez Jr RL / kaledhonkar S / Fu Z / Caban K / Li W / Chen B / Sun M | |||||||||||||||
Funding support | United States, 4 items
| |||||||||||||||
Citation | Journal: Nature / Year: 2019 Title: Late steps in bacterial translation initiation visualized using time-resolved cryo-EM. Authors: Sandip Kaledhonkar / Ziao Fu / Kelvin Caban / Wen Li / Bo Chen / Ming Sun / Ruben L Gonzalez / Joachim Frank / Abstract: The initiation of bacterial translation involves the tightly regulated joining of the 50S ribosomal subunit to an initiator transfer RNA (fMet-tRNA)-containing 30S ribosomal initiation complex to ...The initiation of bacterial translation involves the tightly regulated joining of the 50S ribosomal subunit to an initiator transfer RNA (fMet-tRNA)-containing 30S ribosomal initiation complex to form a 70S initiation complex, which subsequently matures into a 70S elongation-competent complex. Rapid and accurate formation of the 70S initiation complex is promoted by initiation factors, which must dissociate from the 30S initiation complex before the resulting 70S elongation-competent complex can begin the elongation of translation. Although comparisons of the structures of the 30S and 70S initiation complexes have revealed that the ribosome, initiation factors and fMet-tRNA can acquire different conformations in these complexes, the timing of conformational changes during formation of the 70S initiation complex, the structures of any intermediates formed during these rearrangements, and the contributions that these dynamics might make to the mechanism and regulation of initiation remain unknown. Moreover, the absence of a structure of the 70S elongation-competent complex formed via an initiation-factor-catalysed reaction has precluded an understanding of the rearrangements to the ribosome, initiation factors and fMet-tRNA that occur during maturation of a 70S initiation complex into a 70S elongation-competent complex. Here, using time-resolved cryogenic electron microscopy, we report the near-atomic-resolution view of how a time-ordered series of conformational changes drive and regulate subunit joining, initiation factor dissociation and fMet-tRNA positioning during formation of the 70S elongation-competent complex. Our results demonstrate the power of time-resolved cryogenic electron microscopy to determine how a time-ordered series of conformational changes contribute to the mechanism and regulation of one of the most fundamental processes in biology. | |||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0662.map.gz | 6.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-0662-v30.xml emd-0662.xml | 60.7 KB 60.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0662_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_0662.png | 233.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0662 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0662 | HTTPS FTP |
-Validation report
Summary document | emd_0662_validation.pdf.gz | 404.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_0662_full_validation.pdf.gz | 404 KB | Display | |
Data in XML | emd_0662_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | emd_0662_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0662 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0662 | HTTPS FTP |
-Related structure data
Related structure data | 6o9kMC 0643C 0661C 6o7kC 6o9jC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_0662.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | 70S initiation complex with IF2 and P/I tRNA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.66 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
+Entire : 70S elongation competent ribosome
+Supramolecule #1: 70S elongation competent ribosome
+Macromolecule #1: 16S rRNA
+Macromolecule #22: mRNA
+Macromolecule #23: tRNA
+Macromolecule #25: 23S rRNA
+Macromolecule #44: 5S rRNA
+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
+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 S21
+Macromolecule #24: Translation initiation factor IF-2
+Macromolecule #26: 50S ribosomal protein L4
+Macromolecule #27: 50S ribosomal protein L5
+Macromolecule #28: 50S ribosomal protein L10
+Macromolecule #29: 50S ribosomal protein L6
+Macromolecule #30: 50S ribosomal protein L11
+Macromolecule #31: 50S ribosomal protein L13
+Macromolecule #32: 50S ribosomal protein L14
+Macromolecule #33: 50S ribosomal protein L15
+Macromolecule #34: 50S ribosomal protein L16
+Macromolecule #35: 50S ribosomal protein L17
+Macromolecule #36: 50S ribosomal protein L18
+Macromolecule #37: 50S ribosomal protein L19
+Macromolecule #38: 50S ribosomal protein L20
+Macromolecule #39: 50S ribosomal protein L21
+Macromolecule #40: 50S ribosomal protein L22
+Macromolecule #41: 50S ribosomal protein L23
+Macromolecule #42: 50S ribosomal protein L24
+Macromolecule #43: 50S ribosomal protein L25
+Macromolecule #45: 50S ribosomal protein L36
+Macromolecule #46: 50S ribosomal protein L27
+Macromolecule #47: 50S ribosomal protein L28
+Macromolecule #48: 50S ribosomal protein L29
+Macromolecule #49: 50S ribosomal protein L30
+Macromolecule #50: 50S ribosomal protein L3
+Macromolecule #51: 50S ribosomal protein L32
+Macromolecule #52: 50S ribosomal protein L33
+Macromolecule #53: 50S ribosomal protein L34
+Macromolecule #54: 50S ribosomal protein L35
+Macromolecule #55: 50S ribosomal protein L2
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI F30 |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: DARK FIELD |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
---|---|
Output model | PDB-6o9k: |