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Yorodumi- EMDB-17363: Staphylococcus aureus 70S ribosome with elongation factor G locke... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17363 | |||||||||||||||
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Title | Staphylococcus aureus 70S ribosome with elongation factor G locked with fusidic acid cyclopentane in post-translocational state | |||||||||||||||
Map data | Local filtered map | |||||||||||||||
Sample |
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Keywords | RIBOSOME / fusidic acid / EF-G / antibiotic | |||||||||||||||
Function / homology | Function and homology information ribosome disassembly / translation elongation factor activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit ...ribosome disassembly / translation elongation factor activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / transferase activity / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / GTP binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) / Escherichia coli (E. coli) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.44 Å | |||||||||||||||
Authors | Gonzalez-Lopez A / Selmer M | |||||||||||||||
Funding support | Sweden, 4 items
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Citation | Journal: To Be Published Title: Cryo-EM structures of Staphylococcus aureus 70S ribosomes in complex with elongation factor G and fusidic acid Authors: Gonzalez-Lopez A / Larsson D / Nelson B / Hergenrother PJ / Selmer M | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17363.map.gz | 62.2 MB | EMDB map data format | |
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Header (meta data) | emd-17363-v30.xml emd-17363.xml | 85.6 KB 85.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17363_fsc.xml | 26.1 KB | Display | FSC data file |
Images | emd_17363.png | 168.6 KB | ||
Masks | emd_17363_msk_1.map | 1.3 GB | Mask map | |
Filedesc metadata | emd-17363.cif.gz | 16 KB | ||
Others | emd_17363_additional_1.map.gz emd_17363_additional_2.map.gz emd_17363_half_map_1.map.gz emd_17363_half_map_2.map.gz | 654.6 MB 656.8 MB 1.2 GB 1.2 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17363 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17363 | HTTPS FTP |
-Related structure data
Related structure data | 8p2fMC 8p2gC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17363.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Local filtered map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.728 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17363_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Local map around EF-G
File | emd_17363_additional_1.map | ||||||||||||
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Annotation | Local map around EF-G | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_17363_additional_2.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_17363_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_17363_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Staphylococcus aureus 70S ribosome with elongation factor G and f...
+Supramolecule #1: Staphylococcus aureus 70S ribosome with elongation factor G and f...
+Macromolecule #1: 50S ribosomal protein L28
+Macromolecule #2: 50S ribosomal protein L29
+Macromolecule #3: 50S ribosomal protein L30
+Macromolecule #4: 50S ribosomal protein L31 type B
+Macromolecule #5: 50S ribosomal protein L32
+Macromolecule #6: 50S ribosomal protein L33 1
+Macromolecule #7: 50S ribosomal protein L34
+Macromolecule #8: 50S ribosomal protein L35
+Macromolecule #9: 50S ribosomal protein L36
+Macromolecule #13: Elongation factor G
+Macromolecule #14: 50S ribosomal protein L2
+Macromolecule #15: 50S ribosomal protein L3
+Macromolecule #16: 50S ribosomal protein L4
+Macromolecule #17: 50S ribosomal protein L5
+Macromolecule #18: 50S ribosomal protein L6
+Macromolecule #19: 50S ribosomal protein L13
+Macromolecule #20: 50S ribosomal protein L14
+Macromolecule #21: 50S ribosomal protein L15
+Macromolecule #22: 50S ribosomal protein L16
+Macromolecule #23: 50S ribosomal protein L17
+Macromolecule #24: 50S ribosomal protein L18
+Macromolecule #25: 50S ribosomal protein L19
+Macromolecule #26: 50S ribosomal protein L20
+Macromolecule #27: 50S ribosomal protein L21
+Macromolecule #28: 50S ribosomal protein L22
+Macromolecule #29: 50S ribosomal protein L23
+Macromolecule #30: 50S ribosomal protein L24
+Macromolecule #31: 50S ribosomal protein L25
+Macromolecule #32: 50S ribosomal protein L27
+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: 30S ribosomal protein S9
+Macromolecule #43: 30S ribosomal protein S10
+Macromolecule #44: 30S ribosomal protein S11
+Macromolecule #45: 30S ribosomal protein S12
+Macromolecule #46: 30S ribosomal protein S13
+Macromolecule #47: 30S ribosomal protein S14 type Z
+Macromolecule #48: 30S ribosomal protein S15
+Macromolecule #49: 30S ribosomal protein S16
+Macromolecule #50: 30S ribosomal protein S17
+Macromolecule #51: 30S ribosomal protein S18
+Macromolecule #52: 30S ribosomal protein S19
+Macromolecule #53: 30S ribosomal protein S20
+Macromolecule #10: 23S ribosomal RNA
+Macromolecule #11: 5S ribosomal RNA
+Macromolecule #12: tRNA
+Macromolecule #33: 16S ribosomal RNA
+Macromolecule #34: mRNA
+Macromolecule #54: ZINC ION
+Macromolecule #55: MAGNESIUM ION
+Macromolecule #56: SPERMIDINE
+Macromolecule #57: 1,4-DIAMINOBUTANE
+Macromolecule #58: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #59: 2-[(3~{R},4~{S},5~{S},8~{S},9~{S},10~{S},11~{R},13~{S},14~{S},16~...
+Macromolecule #60: POTASSIUM ION
+Macromolecule #61: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa | |||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.4 µm / Calibrated defocus min: 0.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.3 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 165000 |
Specialist optics | Energy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 17252 / Average exposure time: 2.23 sec. / Average electron dose: 27.77 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT | ||||||||||
Output model | PDB-8p2f: |