+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33904 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of 50S-HflX complex | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | HflX / RIBOSOME | |||||||||
Function / homology | Function and homology information ribosome disassembly / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / rescue of stalled ribosome ...ribosome disassembly / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / rescue of stalled ribosome / translational termination / translation repressor activity / ribosome assembly / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / response to heat / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / GTPase activity / negative regulation of DNA-templated transcription / GTP binding / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.52 Å | |||||||||
Authors | Damu W / Ning G | |||||||||
Funding support | China, 1 items
| |||||||||
Citation | Journal: Biorxiv / Year: 2022 Title: Cryo-EM Structure of the 50S-HflX Complex Reveals a Novel Mechanism of Antibiotic Resistance in E. coli Authors: Wu D / Dai Y / Gao N | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_33904.map.gz | 88.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-33904-v30.xml emd-33904.xml | 56.3 KB 56.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33904_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_33904.png | 62.7 KB | ||
Filedesc metadata | emd-33904.cif.gz | 14.9 KB | ||
Others | emd_33904_half_map_1.map.gz emd_33904_half_map_2.map.gz | 80.6 MB 80.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33904 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33904 | HTTPS FTP |
-Related structure data
Related structure data | 7ylaMC 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_33904.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.052 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_33904_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_33904_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : Cryo-EM structure of 50S-HflX
+Supramolecule #1: Cryo-EM structure of 50S-HflX
+Supramolecule #2: 50S ribosome
+Supramolecule #3: GTPase HflX
+Macromolecule #1: GTPase HflX
+Macromolecule #4: 50S ribosomal protein L2
+Macromolecule #5: 50S ribosomal protein L3
+Macromolecule #6: 50S ribosomal protein L4
+Macromolecule #7: 50S ribosomal protein L5
+Macromolecule #8: 50S ribosomal protein L6
+Macromolecule #9: 50S ribosomal protein L9
+Macromolecule #10: 50S ribosomal protein L11
+Macromolecule #11: 50S ribosomal protein L13
+Macromolecule #12: 50S ribosomal protein L14
+Macromolecule #13: 50S ribosomal protein L15
+Macromolecule #14: 50S ribosomal protein L16
+Macromolecule #15: 50S ribosomal protein L17
+Macromolecule #16: 50S ribosomal protein L18
+Macromolecule #17: 50S ribosomal protein L19
+Macromolecule #18: 50S ribosomal protein L20
+Macromolecule #19: 50S ribosomal protein L21
+Macromolecule #20: 50S ribosomal protein L22
+Macromolecule #21: 50S ribosomal protein L23
+Macromolecule #22: 50S ribosomal protein L24
+Macromolecule #23: 50S ribosomal protein L25
+Macromolecule #24: 50S ribosomal protein L27
+Macromolecule #25: 50S ribosomal protein L28
+Macromolecule #26: 50S ribosomal protein L29
+Macromolecule #27: 50S ribosomal protein L30
+Macromolecule #28: 50S ribosomal protein L32
+Macromolecule #29: 50S ribosomal protein L33
+Macromolecule #30: 50S ribosomal protein L34
+Macromolecule #31: 50S ribosomal protein L35
+Macromolecule #32: 50S ribosomal protein L36
+Macromolecule #2: Escherichia coli strain K-12 substr. MG1655_TMP32XR1 chromosome, ...
+Macromolecule #3: 5S rRNA
+Macromolecule #33: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
+Macromolecule #34: MAGNESIUM ION
+Macromolecule #35: SODIUM ION
+Macromolecule #36: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: DIFFRACTION / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.7000000000000001 µm |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 1.8 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |