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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-13245 | |||||||||
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Title | E. faecalis 70S ribosome with P-tRNA, state IV | |||||||||
![]() | 70S ribosome from E. faecalis with P-tRNA, state IV. From RELION Refine3D. | |||||||||
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![]() | Ribosome / Enterococcus faecalis / P-tRNA | |||||||||
Function / homology | ![]() large ribosomal subunit / 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 ...large ribosomal subunit / 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 / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Crowe-McAuliffe C / Wilson DN | |||||||||
Funding support | ![]() ![]()
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![]() | Journal: mSphere / Year: 2018 Title: The Enterococcus Cassette Chromosome, a Genomic Variation Enabler in Enterococci. Authors: A Sivertsen / J Janice / T Pedersen / T M Wagner / J Hegstad / K Hegstad / ![]() Abstract: has a highly variable genome prone to recombination and horizontal gene transfer. Here, we have identified a novel genetic island with an insertion locus and mobilization genes similar to those of ... has a highly variable genome prone to recombination and horizontal gene transfer. Here, we have identified a novel genetic island with an insertion locus and mobilization genes similar to those of staphylococcus cassette chromosome elements SCC This novel element termed the enterococcus cassette chromosome (ECC) element was located in the 3' region of and encoded large serine recombinases similar to SCC Horizontal transfer of an ECC element termed ECC:: containing a knock-in chloramphenicol resistance determinant occurred in the presence of a conjugative plasmid. We determined the ECC:: insertion site in the 3' region of in the recipient by long-read sequencing. ECC:: also mobilized by homologous recombination through sequence identity between flanking insertion sequence (IS) elements in ECC:: and the conjugative plasmid. The genes were found in 69 of 516 genomes in GenBank. Full-length ECC elements were retrieved from 32 of these genomes. ECCs were flanked by and sites of approximately 50 bp. The sequences were found by PCR and sequencing of circularized ECCs in three strains. The genes in ECCs contained an amalgam of common and rare genes. Taken together, our data imply that ECC elements act as hot spots for genetic exchange and contribute to the large variation of accessory genes found in is a bacterium found in a great variety of environments, ranging from the clinic as a nosocomial pathogen to natural habitats such as mammalian intestines, water, and soil. They are known to exchange genetic material through horizontal gene transfer and recombination, leading to great variability of accessory genes and aiding environmental adaptation. Identifying mobile genetic elements causing sequence variation is important to understand how genetic content variation occurs. Here, a novel genetic island, the enterococcus cassette chromosome, is shown to contain a wealth of genes, which may aid in adapting to new environments. The transmission mechanism involves the only two conserved genes within ECC, , large serine recombinases that insert ECC into the host genome similarly to SCC elements found in staphylococci. #1: ![]() Title: Structural basis for PoxtA-mediated resistance to Phenicol and Oxazolidinone antibiotics Authors: Crowe-McAuliffe C / Murina V / Kasari M / Takada H / Turnbull KJ / Sundsfjord A / Hegstad K / Atkinson GC / Wilson DN / Hauryliuk V | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 253 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 74.9 KB 74.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.9 KB | Display | ![]() |
Images | ![]() | 113.2 KB | ||
Masks | ![]() | 282.6 MB | ![]() | |
Filedesc metadata | ![]() | 14 KB | ||
Others | ![]() ![]() ![]() | 41.4 MB 254.6 MB 254.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7p7uMC ![]() 7p7qC ![]() 7p7rC ![]() 7p7sC ![]() 7p7tC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 70S ribosome from E. faecalis with P-tRNA, state IV. From RELION Refine3D. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: 70S ribosome from E. faecalis with P-tRNA, state IV. Sharpened map.
File | emd_13245_additional_1.map | ||||||||||||
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Annotation | 70S ribosome from E. faecalis with P-tRNA, state IV. Sharpened map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: 70S ribosome from E. faecalis with P-tRNA, state IV. Half map.
File | emd_13245_half_map_1.map | ||||||||||||
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Annotation | 70S ribosome from E. faecalis with P-tRNA, state IV. Half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: 70S ribosome from E. faecalis with P-tRNA, state IV. Half map.
File | emd_13245_half_map_2.map | ||||||||||||
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Annotation | 70S ribosome from E. faecalis with P-tRNA, state IV. Half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : 70S ribosome from E. faecalis with P-tRNA (initiation complex), s...
+Supramolecule #1: 70S ribosome from E. faecalis with P-tRNA (initiation complex), s...
+Macromolecule #1: 50S ribosomal protein L29
+Macromolecule #2: 50S ribosomal protein L30
+Macromolecule #3: 50S ribosomal protein L31 type B
+Macromolecule #4: 50S ribosomal protein L32
+Macromolecule #5: 50S ribosomal protein L33
+Macromolecule #6: 50S ribosomal protein L34
+Macromolecule #7: 50S ribosomal protein L35
+Macromolecule #8: 50S ribosomal protein L36
+Macromolecule #12: 50S ribosomal protein L2
+Macromolecule #13: 50S ribosomal protein L3
+Macromolecule #14: 50S ribosomal protein L4
+Macromolecule #15: 50S ribosomal protein L5
+Macromolecule #16: 50S ribosomal protein L6
+Macromolecule #17: 50S ribosomal protein L13
+Macromolecule #18: 50S ribosomal protein L14
+Macromolecule #19: 50S ribosomal protein L15
+Macromolecule #20: 50S ribosomal protein L16
+Macromolecule #21: 50S ribosomal protein L17
+Macromolecule #22: 50S ribosomal protein L18
+Macromolecule #23: 50S ribosomal protein L19
+Macromolecule #24: 50S ribosomal protein L20
+Macromolecule #25: 50S ribosomal protein L21
+Macromolecule #26: 50S ribosomal protein L22
+Macromolecule #27: 50S ribosomal protein L23
+Macromolecule #28: 50S ribosomal protein L24
+Macromolecule #29: 50S ribosomal protein L27
+Macromolecule #30: 50S ribosomal protein L28
+Macromolecule #33: 30S ribosomal protein S2
+Macromolecule #34: 30S ribosomal protein S3
+Macromolecule #35: 30S ribosomal protein S4
+Macromolecule #36: 30S ribosomal protein S5
+Macromolecule #37: 30S ribosomal protein S6
+Macromolecule #38: 30S ribosomal protein S7
+Macromolecule #39: 30S ribosomal protein S8
+Macromolecule #40: 30S ribosomal protein S9
+Macromolecule #41: 30S ribosomal protein S10
+Macromolecule #42: 30S ribosomal protein S11
+Macromolecule #43: 30S ribosomal protein S12
+Macromolecule #44: 30S ribosomal protein S13
+Macromolecule #45: 30S ribosomal protein S14 type Z
+Macromolecule #46: 30S ribosomal protein S15
+Macromolecule #47: 30S ribosomal protein S16
+Macromolecule #48: 30S ribosomal protein S17
+Macromolecule #49: 30S ribosomal protein S18
+Macromolecule #50: 30S ribosomal protein S19
+Macromolecule #51: 30S ribosomal protein S20
+Macromolecule #9: 23S rRNA
+Macromolecule #10: 5S rRNA
+Macromolecule #11: tRNA-fMet
+Macromolecule #31: 16S rRNA
+Macromolecule #32: mRNA
+Macromolecule #52: ZINC ION
+Macromolecule #53: POTASSIUM ION
+Macromolecule #54: MAGNESIUM ION
+Macromolecule #55: 1,4-DIAMINOBUTANE
+Macromolecule #56: SPECTINOMYCIN
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 9 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK II |
Details | Grid was prepared by four applications of elution fraction from affinity purification. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 3639 / Average exposure time: 5.0 sec. / Average electron dose: 30.255 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |