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Yorodumi- EMDB-3852: Elongation factor G-ribosome complex captures in the absence of i... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3852 | |||||||||
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Title | Elongation factor G-ribosome complex captures in the absence of inhibitors. | |||||||||
Map data | Elongation factor G-ribosome complex captured in the absence of inhibitors | |||||||||
Sample |
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Function / homology | Function and homology information translation elongation factor activity / large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / small ribosomal subunit / 5S rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly ...translation elongation factor activity / large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / small ribosomal subunit / 5S rRNA binding / transferase activity / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermus thermophilus HB8 (bacteria) / Escherichia coli (E. coli) / Thermus thermophilus (bacteria) / Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Mace K / Giudice E / Chat S / Gillet R | |||||||||
Citation | Journal: Nucleic Acids Res / Year: 2018 Title: The structure of an elongation factor G-ribosome complex captured in the absence of inhibitors. Authors: Kevin Macé / Emmanuel Giudice / Sophie Chat / Reynald Gillet / Abstract: During translation's elongation cycle, elongation factor G (EF-G) promotes messenger and transfer RNA translocation through the ribosome. Until now, the structures reported for EF-G-ribosome ...During translation's elongation cycle, elongation factor G (EF-G) promotes messenger and transfer RNA translocation through the ribosome. Until now, the structures reported for EF-G-ribosome complexes have been obtained by trapping EF-G in the ribosome. These results were based on use of non-hydrolyzable guanosine 5'-triphosphate (GTP) analogs, specific inhibitors or a mutated EF-G form. Here, we present the first cryo-electron microscopy structure of EF-G bound to ribosome in the absence of an inhibitor. The structure reveals a natural conformation of EF-G·GDP in the ribosome, with a previously unseen conformation of its third domain. These data show how EF-G must affect translocation, and suggest the molecular mechanism by which fusidic acid antibiotic prevents the release of EF-G after GTP hydrolysis. | |||||||||
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_3852.map.gz | 25.1 MB | EMDB map data format | |
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Header (meta data) | emd-3852-v30.xml emd-3852.xml | 88.9 KB 88.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3852_fsc.xml | 14.5 KB | Display | FSC data file |
Images | emd_3852.png | 79.6 KB | ||
Others | emd_3852_half_map_1.map.gz emd_3852_half_map_2.map.gz | 225.6 MB 226.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3852 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3852 | HTTPS FTP |
-Validation report
Summary document | emd_3852_validation.pdf.gz | 418.5 KB | Display | EMDB validaton report |
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Full document | emd_3852_full_validation.pdf.gz | 417.6 KB | Display | |
Data in XML | emd_3852_validation.xml.gz | 20.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3852 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3852 | HTTPS FTP |
-Related structure data
Related structure data | 5ot7MC 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_3852.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Elongation factor G-ribosome complex captured in the absence of inhibitors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1025 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: unfiltered, unmasked half map 2
File | emd_3852_half_map_1.map | ||||||||||||
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Annotation | unfiltered, unmasked half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: unfiltered, unmasked half map 1
File | emd_3852_half_map_2.map | ||||||||||||
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Annotation | unfiltered, unmasked half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : EF-G bound to 70S ribosome
+Supramolecule #1: EF-G bound to 70S ribosome
+Supramolecule #2: 70S ribosome
+Supramolecule #3: tRNA PHE
+Supramolecule #4: Elongation factor G
+Supramolecule #5: mRNA
+Macromolecule #1: 16S Ribosomal RNA
+Macromolecule #2: tRNA-Phe
+Macromolecule #3: mRNA
+Macromolecule #4: 23S Ribosomal RNA
+Macromolecule #5: 5S Ribosomal RNA
+Macromolecule #6: 50S ribosomal protein L25
+Macromolecule #7: 50S ribosomal protein L9
+Macromolecule #8: 30S ribosomal protein S2
+Macromolecule #9: 30S ribosomal protein S3
+Macromolecule #10: 30S ribosomal protein S4
+Macromolecule #11: 30S ribosomal protein S5
+Macromolecule #12: 30S ribosomal protein S6
+Macromolecule #13: 30S ribosomal protein S7
+Macromolecule #14: 30S ribosomal protein S8
+Macromolecule #15: 30S ribosomal protein S9
+Macromolecule #16: 30S ribosomal protein S10
+Macromolecule #17: 30S ribosomal protein S11
+Macromolecule #18: 30S ribosomal protein S12
+Macromolecule #19: 30S ribosomal protein S13
+Macromolecule #20: 30S ribosomal protein S14 type Z
+Macromolecule #21: 30S ribosomal protein S15
+Macromolecule #22: 30S ribosomal protein S16
+Macromolecule #23: 30S ribosomal protein S17
+Macromolecule #24: 30S ribosomal protein S18
+Macromolecule #25: 30S ribosomal protein S19
+Macromolecule #26: 30S ribosomal protein S20
+Macromolecule #27: 30S ribosomal protein Thx
+Macromolecule #28: Elongation factor G
+Macromolecule #29: 50S ribosomal protein L27
+Macromolecule #30: 50S ribosomal protein L28
+Macromolecule #31: 50S ribosomal protein L29
+Macromolecule #32: 50S ribosomal protein L30
+Macromolecule #33: 50S ribosomal protein L31
+Macromolecule #34: 50S ribosomal protein L32
+Macromolecule #35: 50S ribosomal protein L33
+Macromolecule #36: 50S ribosomal protein L34
+Macromolecule #37: 50S ribosomal protein L35
+Macromolecule #38: 50S ribosomal protein L36
+Macromolecule #39: 50S ribosomal protein L1
+Macromolecule #40: 50S ribosomal protein L2
+Macromolecule #41: 50S ribosomal protein L3
+Macromolecule #42: 50S ribosomal protein L4
+Macromolecule #43: 50S ribosomal protein L5
+Macromolecule #44: 50S ribosomal protein L6
+Macromolecule #45: Ribosomal protein uL10
+Macromolecule #46: Ribosomal protein uL11
+Macromolecule #47: Ribosomal protein bL12
+Macromolecule #48: 50S ribosomal protein L13
+Macromolecule #49: 50S ribosomal protein L14
+Macromolecule #50: 50S ribosomal protein L15
+Macromolecule #51: 50S ribosomal protein L16
+Macromolecule #52: 50S ribosomal protein L17
+Macromolecule #53: 50S ribosomal protein L18
+Macromolecule #54: 50S ribosomal protein L19
+Macromolecule #55: 50S ribosomal protein L20
+Macromolecule #56: 50S ribosomal protein L21
+Macromolecule #57: 50S ribosomal protein L22
+Macromolecule #58: 50S ribosomal protein L23
+Macromolecule #59: 50S ribosomal protein L24
+Macromolecule #60: MAGNESIUM ION
+Macromolecule #61: ZINC ION
+Macromolecule #62: GUANOSINE-5'-DIPHOSPHATE
-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 R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.04 kPa | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 303 K / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Spherical aberration corrector: CS-corrected |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Frames/image: 1-7 / Number grids imaged: 1 / Number real images: 949 / Average exposure time: 1.0 sec. / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.7 µm / Calibrated defocus min: 0.4 µm / Calibrated magnification: 120443 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.0023 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Details | each ribosomal rna and protein was first rigid body fitted in the map using UCSF chimera. The missing componant (mRNA and bL9) were then added and fitted. the quality of the fitting was then assesed and adjust manually, residue per residue using coot. the RNA confomation were ajusted with the ERRASER modul (in Phenix). The final model was refined using phenix real space refinement procedure. |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient |
Output model | PDB-5ot7: |