+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18145 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of arbekacin bound Escherichia coli 70S ribosome | |||||||||||||||
Map data | E. coli 70S-fMet-tRNA-mRNA-arbekacin complex | |||||||||||||||
Sample |
| |||||||||||||||
Keywords | arbekacin / ribosome / protein synthesis inhibitor / aminoglycoside | |||||||||||||||
Function / homology | Function and homology information negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis ...negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / four-way junction DNA binding / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / 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 / transcription antitermination / response to reactive oxygen species / translational initiation / regulation of cell growth / ribosomal large subunit assembly / 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 / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Escherichia coli (E. coli) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||
Authors | Majumdar S / Parajuli NP / Ge X / Emmerich A / Sanyal S | |||||||||||||||
Funding support | Sweden, 4 items
| |||||||||||||||
Citation | Journal: To be published Title: Structure of arbekacin bound Escherichia coli 70S ribosome Authors: Majumdar S / Parajuli NP / Ge X / Emmerich A / Sanyal S | |||||||||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_18145.map.gz | 55.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-18145-v30.xml emd-18145.xml | 70.8 KB 70.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18145_fsc.xml | 17.7 KB | Display | FSC data file |
Images | emd_18145.png | 101.5 KB | ||
Filedesc metadata | emd-18145.cif.gz | 13.3 KB | ||
Others | emd_18145_additional_1.map.gz emd_18145_half_map_1.map.gz emd_18145_half_map_2.map.gz | 233.9 MB 381 MB 381.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18145 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18145 | HTTPS FTP |
-Related structure data
Related structure data | 8q4fMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_18145.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | E. coli 70S-fMet-tRNA-mRNA-arbekacin complex | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8513 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Sample components
+Entire : Escherichia coli 70S ribosome bound to fret-tRNA mRNA
+Supramolecule #1: Escherichia coli 70S ribosome bound to fret-tRNA mRNA
+Macromolecule #1: Large ribosomal subunit protein bL33
+Macromolecule #2: Large ribosomal subunit protein bL34
+Macromolecule #3: Large ribosomal subunit protein bL35
+Macromolecule #4: Large ribosomal subunit protein bL36A
+Macromolecule #5: Large ribosomal subunit protein bL31A
+Macromolecule #7: Small ribosomal subunit protein uS2
+Macromolecule #8: Small ribosomal subunit protein uS3
+Macromolecule #9: Small ribosomal subunit protein uS4
+Macromolecule #10: Small ribosomal subunit protein uS5
+Macromolecule #11: Small ribosomal subunit protein bS6, fully modified isoform
+Macromolecule #12: Small ribosomal subunit protein uS7
+Macromolecule #13: Small ribosomal subunit protein uS8
+Macromolecule #14: Small ribosomal subunit protein uS9
+Macromolecule #15: Small ribosomal subunit protein uS10
+Macromolecule #16: Small ribosomal subunit protein uS11
+Macromolecule #17: Small ribosomal subunit protein uS12
+Macromolecule #18: Small ribosomal subunit protein uS13
+Macromolecule #19: Small ribosomal subunit protein uS14
+Macromolecule #20: Small ribosomal subunit protein uS15
+Macromolecule #21: Small ribosomal subunit protein bS16
+Macromolecule #22: Small ribosomal subunit protein uS17
+Macromolecule #23: Small ribosomal subunit protein bS18
+Macromolecule #24: Small ribosomal subunit protein uS19
+Macromolecule #25: Small ribosomal subunit protein bS20
+Macromolecule #26: Small ribosomal subunit protein bS21
+Macromolecule #31: Large ribosomal subunit protein uL2
+Macromolecule #32: 50S ribosomal protein L3
+Macromolecule #33: Large ribosomal subunit protein uL4
+Macromolecule #34: Large ribosomal subunit protein uL5
+Macromolecule #35: Large ribosomal subunit protein uL6
+Macromolecule #36: Large ribosomal subunit protein uL13
+Macromolecule #37: Large ribosomal subunit protein uL14
+Macromolecule #38: Large ribosomal subunit protein uL15
+Macromolecule #39: 50S ribosomal protein L16
+Macromolecule #40: Large ribosomal subunit protein bL17
+Macromolecule #41: Large ribosomal subunit protein uL18
+Macromolecule #42: Large ribosomal subunit protein bL19
+Macromolecule #43: Large ribosomal subunit protein bL20
+Macromolecule #44: Large ribosomal subunit protein bL21
+Macromolecule #45: Large ribosomal subunit protein uL23
+Macromolecule #46: Large ribosomal subunit protein uL24
+Macromolecule #47: Large ribosomal subunit protein bL25
+Macromolecule #48: Large ribosomal subunit protein bL27
+Macromolecule #49: Large ribosomal subunit protein bL28
+Macromolecule #50: Large ribosomal subunit protein uL29
+Macromolecule #51: Large ribosomal subunit protein uL30
+Macromolecule #52: Large ribosomal subunit protein bL32
+Macromolecule #6: 16S rRNA
+Macromolecule #27: mRNA
+Macromolecule #28: tRNA-fMet
+Macromolecule #29: 23S rRNA
+Macromolecule #30: 5S rRNA
+Macromolecule #53: Arbekacin
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Software | Name: EPU (ver. v2.11.1) |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.37 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |