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Yorodumi- EMDB-74431: Escherichia coli 70S ribosome initiation complex bound to IF1 and... -
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Open data
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Basic information
| Entry | ![]() | |||||||||||||||
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| Title | Escherichia coli 70S ribosome initiation complex bound to IF1 and extended IF2-GDPCP (70S IC*) | |||||||||||||||
Map data | Cryo-EM map of E.coli 70S ribosome bound to IF1 and extended IF2 (70S IC*) | |||||||||||||||
Sample |
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Keywords | E.coli / 70S / IF1 / IF2 / cryo-EM / tRNA / RIBOSOME | |||||||||||||||
| Function / homology | Function and homology informationguanosine tetraphosphate binding / negative regulation of cytoplasmic translational initiation / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / translation repressor activity / translation initiation factor activity / negative regulation of translational initiation ...guanosine tetraphosphate binding / negative regulation of cytoplasmic translational initiation / transcriptional attenuation / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / translation repressor activity / translation initiation factor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / cytosolic ribosome assembly / ribosome assembly / assembly of large subunit precursor of preribosome / transcription antitermination / regulation of cell growth / translational initiation / DNA-templated transcription termination / response to radiation / maintenance of translational fidelity / mRNA 5'-UTR binding / transferase activity / large ribosomal subunit / ribosomal small subunit assembly / ribosome binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / tRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribonucleoprotein complex / ribosome / translation / structural constituent of ribosome / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / GTPase activity / GTP binding / DNA binding / RNA binding / metal ion binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
| Biological species | ![]() Escherichia phage T4 (virus) | |||||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||||||||
Authors | Basu RS / Valdez NA / Guerra GS / Demo G / Gagnon MG | |||||||||||||||
| Funding support | United States, Czech Republic, 4 items
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Citation | Journal: To Be PublishedTitle: Time-resolved visualization of IF1- and IF2-driven translation initiation in bacteria Authors: Guerra GS / Zafar H / Ge X / Basu RS / Huang C / Hassan A / Valdez NA / Brabencova S / Slamova L / Mandava CS / Gamper H / Hou Y / Gagnon MG / Sanyal S / Demo G | |||||||||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_74431.map.gz | 255.6 MB | EMDB map data format | |
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| Header (meta data) | emd-74431-v30.xml emd-74431.xml | 82.5 KB 82.5 KB | Display Display | EMDB header |
| Images | emd_74431.png | 65.2 KB | ||
| Masks | emd_74431_msk_1.map | 512 MB | Mask map | |
| Filedesc metadata | emd-74431.cif.gz | 16.1 KB | ||
| Others | emd_74431_additional_1.map.gz emd_74431_half_map_1.map.gz emd_74431_half_map_2.map.gz | 483.5 MB 474.7 MB 474.7 MB | ||
| Archive directory | https://data.pdbj.org/pub/emdb/structures/EMD-74431 ftp://data.pdbj.org/pub/emdb/structures/EMD-74431 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9zn2MC ![]() 9tknC ![]() 9tkoC ![]() 9tkpC ![]() 9tkqC ![]() 9tkrC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_74431.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | Cryo-EM map of E.coli 70S ribosome bound to IF1 and extended IF2 (70S IC*) | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.8623 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Mask #1
| File | emd_74431_msk_1.map | ||||||||||||
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| Projections & Slices |
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| Density Histograms |
-Additional map: Sharpened EM map of E.coli 70S ribosome bound...
| File | emd_74431_additional_1.map | ||||||||||||
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| Annotation | Sharpened EM map of E.coli 70S ribosome bound to IF1 and extended IF2 (70S IC*) | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: EM half map of E.coli 70S ribosome bound...
| File | emd_74431_half_map_1.map | ||||||||||||
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| Annotation | EM half map of E.coli 70S ribosome bound to IF1 and extended IF2 (70S IC*) | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: EM half map of E.coli 70S ribosome bound...
| File | emd_74431_half_map_2.map | ||||||||||||
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| Annotation | EM half map of E.coli 70S ribosome bound to IF1 and extended IF2 (70S IC*) | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
+Entire : E.coli 70S ribosome bound to IF1 and extended IF2
+Supramolecule #1: E.coli 70S ribosome bound to IF1 and extended IF2
+Macromolecule #1: 16S Ribosomal RNA
+Macromolecule #22: 24MF mRNA
+Macromolecule #23: initiator tRNA fMet, DNA (5'-R(P*A)-3')
+Macromolecule #26: 23S Ribosomal RNA
+Macromolecule #27: 5S Ribosomal RNA
+Macromolecule #2: 30S ribosomal protein S2
+Macromolecule #3: 30S ribosomal protein S3
+Macromolecule #4: Small ribosomal subunit protein uS4
+Macromolecule #5: Small ribosomal subunit protein uS5
+Macromolecule #6: 30S ribosomal protein S6
+Macromolecule #7: 30S ribosomal protein S7
+Macromolecule #8: Small ribosomal subunit protein uS8
+Macromolecule #9: Small ribosomal subunit protein uS9
+Macromolecule #10: Small ribosomal subunit protein uS10
+Macromolecule #11: Small ribosomal subunit protein uS11
+Macromolecule #12: Small ribosomal subunit protein uS12
+Macromolecule #13: Small ribosomal subunit protein uS13
+Macromolecule #14: Small ribosomal subunit protein uS14
+Macromolecule #15: Small ribosomal subunit protein uS15
+Macromolecule #16: Small ribosomal subunit protein bS16
+Macromolecule #17: Small ribosomal subunit protein uS17
+Macromolecule #18: Small ribosomal subunit protein bS18
+Macromolecule #19: Small ribosomal subunit protein uS19
+Macromolecule #20: Small ribosomal subunit protein bS20
+Macromolecule #21: Small ribosomal subunit protein bS21
+Macromolecule #24: Translation initiation factor IF-2
+Macromolecule #25: Translation initiation factor IF-1
+Macromolecule #28: 50S ribosomal protein L2
+Macromolecule #29: 50S ribosomal protein L3
+Macromolecule #30: Large ribosomal subunit protein uL4
+Macromolecule #31: Large ribosomal subunit protein uL5
+Macromolecule #32: Large ribosomal subunit protein uL6
+Macromolecule #33: Large ribosomal subunit protein bL9
+Macromolecule #34: Large ribosomal subunit protein uL13
+Macromolecule #35: Large ribosomal subunit protein uL14
+Macromolecule #36: 50S ribosomal protein L15
+Macromolecule #37: Large ribosomal subunit protein uL16
+Macromolecule #38: Large ribosomal subunit protein bL17
+Macromolecule #39: Large ribosomal subunit protein uL18
+Macromolecule #40: Large ribosomal subunit protein bL19
+Macromolecule #41: 50S ribosomal protein L20
+Macromolecule #42: Ribosomal protein L21
+Macromolecule #43: 50S ribosomal protein L22
+Macromolecule #44: 50S ribosomal protein L23
+Macromolecule #45: 50S ribosomal protein L24
+Macromolecule #46: Large ribosomal subunit protein bL25
+Macromolecule #47: 50S ribosomal protein L27
+Macromolecule #48: 50S ribosomal protein L28
+Macromolecule #49: Large ribosomal subunit protein uL29
+Macromolecule #50: 50S ribosomal protein L30
+Macromolecule #51: 50S ribosomal protein L31
+Macromolecule #52: 50S ribosomal protein L32
+Macromolecule #53: 50S ribosomal protein L33
+Macromolecule #54: 50S ribosomal protein L34
+Macromolecule #55: 50S ribosomal protein L35
+Macromolecule #56: 50S ribosomal protein L36
+Macromolecule #57: MAGNESIUM ION
+Macromolecule #58: N-FORMYLMETHIONINE
+Macromolecule #59: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
+Macromolecule #60: ZINC ION
+Macromolecule #61: water
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Concentration | 5 mg/mL |
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| Buffer | pH: 7.5 |
| Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec. / Pretreatment - Atmosphere: OTHER |
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 295 K / Instrument: LEICA EM GP |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
| Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 12290 / Average exposure time: 1.68 sec. / Average electron dose: 40.299 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000 |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Escherichia phage T4 (virus)
Authors
United States,
Czech Republic, 4 items
Citation





















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Processing
FIELD EMISSION GUN

