+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3581 | |||||||||
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Title | Structure of 70S ribosome from Lactococcus lactis | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ribosome / 70S / lactoccocus lactis / Cryo-EM | |||||||||
Function / homology | Function and homology information primary metabolic process / ribosomal large subunit assembly / large ribosomal subunit / regulation of translation / small ribosomal subunit / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome ...primary metabolic process / ribosomal large subunit assembly / large ribosomal subunit / regulation of translation / small ribosomal subunit / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Lactococcus lactis (lactic acid bacteria) / Lactococcus lactis subsp. cremoris MG1363 (lactic acid bacteria) / Lactococcus lactis subsp. cremoris (strain MG1363) (lactic acid bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.6 Å | |||||||||
Authors | Franken LE / Oostergetel GT | |||||||||
Funding support | Netherlands, 2 items
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Citation | Journal: Nat Commun / Year: 2017 Title: A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy. Authors: Linda E Franken / Gert T Oostergetel / Tjaard Pijning / Pranav Puri / Valentina Arkhipova / Egbert J Boekema / Bert Poolman / Albert Guskov / Abstract: Bacteria downregulate their ribosomal activity through dimerization of 70S ribosomes, yielding inactive 100S complexes. In Escherichia coli, dimerization is mediated by the hibernation promotion ...Bacteria downregulate their ribosomal activity through dimerization of 70S ribosomes, yielding inactive 100S complexes. In Escherichia coli, dimerization is mediated by the hibernation promotion factor (HPF) and ribosome modulation factor. Here we report the cryo-electron microscopy study on 100S ribosomes from Lactococcus lactis and a dimerization mechanism involving a single protein: HPF. The N-terminal domain of HPF binds at the same site as HPF in Escherichia coli 100S ribosomes. Contrary to ribosome modulation factor, the C-terminal domain of HPF binds exactly at the dimer interface. Furthermore, ribosomes from Lactococcus lactis do not undergo conformational changes in the 30S head domains upon binding of HPF, and the Shine-Dalgarno sequence and mRNA entrance tunnel remain accessible. Ribosome activity is blocked by HPF due to the inhibition of mRNA recognition by the platform binding center. Phylogenetic analysis of HPF proteins suggests that HPF-mediated dimerization is a widespread mechanism of ribosome hibernation in bacteria.When bacteria enter the stationary growth phase, protein translation is suppressed via the dimerization of 70S ribosomes into inactive complexes. Here the authors provide a structural basis for how the dual domain hibernation promotion factor promotes ribosome dimerization and hibernation in bacteria. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3581.map.gz | 61.7 MB | EMDB map data format | |
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Header (meta data) | emd-3581-v30.xml emd-3581.xml | 66.7 KB 66.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3581_fsc.xml | 20.8 KB | Display | FSC data file |
Images | emd_3581.png | 269.8 KB | ||
Filedesc metadata | emd-3581.cif.gz | 12.8 KB | ||
Others | emd_3581_additional.map.gz | 33 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3581 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3581 | HTTPS FTP |
-Related structure data
Related structure data | 5myjMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3581.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.105 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Supplemental map: emd 3581 additional.map
File | emd_3581_additional.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 70S ribosome
+Supramolecule #1: 70S ribosome
+Macromolecule #1: 16S ribosomal RNA
+Macromolecule #31: 23S ribosomal RNA
+Macromolecule #32: 5S ribosomal RNA
+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 type Z
+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 #22: 50S ribosomal protein L28
+Macromolecule #23: 50S ribosomal protein L29
+Macromolecule #24: 50S ribosomal protein L30
+Macromolecule #25: 50S ribosomal protein L31 type B
+Macromolecule #26: 50S ribosomal protein L32
+Macromolecule #27: 50S ribosomal protein L33 3
+Macromolecule #28: 50S ribosomal protein L34
+Macromolecule #29: 50S ribosomal protein L35
+Macromolecule #30: 50S ribosomal protein L36
+Macromolecule #33: 50S ribosomal protein L2
+Macromolecule #34: 50S ribosomal protein L3
+Macromolecule #35: 50S ribosomal protein L4
+Macromolecule #36: 50S ribosomal protein L5
+Macromolecule #37: 50S ribosomal protein L6
+Macromolecule #38: 50S ribosomal protein L13
+Macromolecule #39: 50S ribosomal protein L14
+Macromolecule #40: 50S ribosomal protein L15
+Macromolecule #41: 50S ribosomal protein L16
+Macromolecule #42: 50S ribosomal protein L17
+Macromolecule #43: 50S ribosomal protein L18
+Macromolecule #44: 50S ribosomal protein L19
+Macromolecule #45: 50S ribosomal protein L20
+Macromolecule #46: 50S ribosomal protein L21
+Macromolecule #47: 50S ribosomal protein L22
+Macromolecule #48: 50S ribosomal protein L23
+Macromolecule #49: 50S ribosomal protein L24
+Macromolecule #50: 50S ribosomal protein L27
+Macromolecule #51: Ribosome hibernation promotion factor
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 291.15 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Specialist optics | Spherical aberration corrector: Cs-corrector (CEOS, Heidelberg, Germany) |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 25.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-5myj: |