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Yorodumi- EMDB-43549: E. coli 70S ribosome with unmodified Lys-tRNAPro(GGG) in the P/P ... -
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Open data
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Basic information
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| Title | E. coli 70S ribosome with unmodified Lys-tRNAPro(GGG) in the P/P conformation on a slippery CCC-C codon | ||||||||||||
Map data | E. coli 70S ribosome with unmodified Lys-tRNAPro(GGG) in the P/P conformation on a slippery CCC-C codon | ||||||||||||
Sample |
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Keywords | 70S ribosome / tRNA / frameshift / RIBOSOME | ||||||||||||
| Function / homology | Function and homology informationnegative regulation of cytoplasmic translational initiation / DnaA-L2 complex / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosome assembly / transcription antitermination / translational initiation ...negative regulation of cytoplasmic translational initiation / DnaA-L2 complex / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosome assembly / transcription antitermination / translational initiation / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
| Biological species | ![]() | ||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||
Authors | Kimbrough EM / Dunham CM / Nguyen HA | ||||||||||||
| Funding support | United States, 3 items
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Citation | Journal: To Be PublishedTitle: The influence of EF-P on mRNA reading frame maintenance Authors: Kimbrough EM / Nguyen HA / Li H / Gamper H / Hou YM / Gonzalez RL / Dunham CM | ||||||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_43549.map.gz | 410.9 MB | EMDB map data format | |
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| Header (meta data) | emd-43549-v30.xml emd-43549.xml | 72.7 KB 72.7 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_43549_fsc.xml | 18.1 KB | Display | FSC data file |
| Images | emd_43549.png | 61.9 KB | ||
| Filedesc metadata | emd-43549.cif.gz | 14 KB | ||
| Others | emd_43549_additional_1.map.gz emd_43549_half_map_1.map.gz emd_43549_half_map_2.map.gz | 476.5 MB 411.7 MB 411 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43549 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43549 | HTTPS FTP |
-Validation report
| Summary document | emd_43549_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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| Full document | emd_43549_full_validation.pdf.gz | 1.2 MB | Display | |
| Data in XML | emd_43549_validation.xml.gz | 26.3 KB | Display | |
| Data in CIF | emd_43549_validation.cif.gz | 35.2 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43549 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43549 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8vv4MC ![]() 8vupC ![]() 8vwqC ![]() 8w2nC 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_43549.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | E. coli 70S ribosome with unmodified Lys-tRNAPro(GGG) in the P/P conformation on a slippery CCC-C codon | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.0691 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Additional map: Additional Map
| File | emd_43549_additional_1.map | ||||||||||||
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| Annotation | Additional Map | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: Half map A
| File | emd_43549_half_map_1.map | ||||||||||||
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| Annotation | Half map A | ||||||||||||
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| Density Histograms |
-Half map: Half map B
| File | emd_43549_half_map_2.map | ||||||||||||
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| Annotation | Half map B | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
+Entire : E.coli 70S complex with mRNA and e*/E-tRNA
+Supramolecule #1: E.coli 70S complex with mRNA and e*/E-tRNA
+Macromolecule #1: 23S ribosomal RNA
+Macromolecule #2: 16S ribosomal RNA
+Macromolecule #3: 5S ribosomal RNA
+Macromolecule #4: mRNA
+Macromolecule #5: tRNA^ProL (GGG)
+Macromolecule #6: 50S ribosomal protein L2
+Macromolecule #7: 50S ribosomal protein L3
+Macromolecule #8: 50S ribosomal protein L4
+Macromolecule #9: 50S ribosomal protein L5
+Macromolecule #10: 50S ribosomal protein L6
+Macromolecule #11: Large ribosomal subunit protein bL9
+Macromolecule #12: 50S ribosomal protein L13
+Macromolecule #13: 50S ribosomal protein L14
+Macromolecule #14: 50S ribosomal protein L15
+Macromolecule #15: 50S ribosomal protein L16
+Macromolecule #16: Large ribosomal subunit protein bL17
+Macromolecule #17: 50S ribosomal protein L18
+Macromolecule #18: 50S ribosomal protein L19
+Macromolecule #19: 50S ribosomal protein L20
+Macromolecule #20: Ribosomal protein L21
+Macromolecule #21: 50S ribosomal protein L22
+Macromolecule #22: 50S ribosomal protein L23
+Macromolecule #23: 50S ribosomal protein L24
+Macromolecule #24: 50S ribosomal protein L25
+Macromolecule #25: Large ribosomal subunit protein bL27
+Macromolecule #26: 50S ribosomal protein L28
+Macromolecule #27: 50S ribosomal protein L29
+Macromolecule #28: Large ribosomal subunit protein uL30
+Macromolecule #29: 50S ribosomal protein L31
+Macromolecule #30: 50S ribosomal protein L32
+Macromolecule #31: Large ribosomal subunit protein bL33
+Macromolecule #32: 50S ribosomal protein L34
+Macromolecule #33: 50S ribosomal protein L35
+Macromolecule #34: 50S ribosomal protein L36
+Macromolecule #35: 30S ribosomal protein S2
+Macromolecule #36: 30S ribosomal protein S3
+Macromolecule #37: 30S ribosomal protein S4
+Macromolecule #38: 30S ribosomal protein S5
+Macromolecule #39: 30S ribosomal protein S6
+Macromolecule #40: 30S ribosomal protein S7
+Macromolecule #41: 30S ribosomal protein S8
+Macromolecule #42: Small ribosomal subunit protein uS9
+Macromolecule #43: 30S ribosomal protein S10
+Macromolecule #44: 30S ribosomal protein S11
+Macromolecule #45: Small ribosomal subunit protein uS12
+Macromolecule #46: 30S ribosomal protein S13
+Macromolecule #47: Small ribosomal subunit protein uS14
+Macromolecule #48: Small ribosomal subunit protein uS15
+Macromolecule #49: 30S ribosomal protein S16
+Macromolecule #50: Small ribosomal subunit protein uS17
+Macromolecule #51: 30S ribosomal protein S18
+Macromolecule #52: 30S ribosomal protein S19
+Macromolecule #53: 30S ribosomal protein S20
+Macromolecule #54: 30S ribosomal protein S21
+Macromolecule #55: MAGNESIUM ION
+Macromolecule #56: LYSINE
+Macromolecule #57: 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
| Buffer | pH: 7.6 |
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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 K3 BIOQUANTUM (6k x 4k) / Average electron dose: 56.07 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Authors
United States, 3 items
Citation










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Processing
FIELD EMISSION GUN


