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Yorodumi- EMDB-25415: Late translocation intermediate with EF-G dissociated (Structure VI) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25415 | |||||||||||||||
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Title | Late translocation intermediate with EF-G dissociated (Structure VI) | |||||||||||||||
Map data | main map used in refinement; blocfiltered and sharpened to -50 at 3.8A | |||||||||||||||
Sample |
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Keywords | Ribosome / Hybrid / Translocation | |||||||||||||||
Function / homology | Function and homology information stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis ...stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / four-way junction DNA binding / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / 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 / molecular adaptor activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||||||||
Authors | Carbone CE / Korostelev AA | |||||||||||||||
Funding support | Czech Republic, 4 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP. Authors: Christine E Carbone / Anna B Loveland / Howard B Gamper / Ya-Ming Hou / Gabriel Demo / Andrei A Korostelev / Abstract: During translation, a conserved GTPase elongation factor-EF-G in bacteria or eEF2 in eukaryotes-translocates tRNA and mRNA through the ribosome. EF-G has been proposed to act as a flexible motor that ...During translation, a conserved GTPase elongation factor-EF-G in bacteria or eEF2 in eukaryotes-translocates tRNA and mRNA through the ribosome. EF-G has been proposed to act as a flexible motor that propels tRNA and mRNA movement, as a rigid pawl that biases unidirectional translocation resulting from ribosome rearrangements, or by various combinations of motor- and pawl-like mechanisms. Using time-resolved cryo-EM, we visualized GTP-catalyzed translocation without inhibitors, capturing elusive structures of ribosome•EF-G intermediates at near-atomic resolution. Prior to translocation, EF-G binds near peptidyl-tRNA, while the rotated 30S subunit stabilizes the EF-G GTPase center. Reverse 30S rotation releases Pi and translocates peptidyl-tRNA and EF-G by ~20 Å. An additional 4-Å translocation initiates EF-G dissociation from a transient ribosome state with highly swiveled 30S head. The structures visualize how nearly rigid EF-G rectifies inherent and spontaneous ribosomal dynamics into tRNA-mRNA translocation, whereas GTP hydrolysis and Pi release drive EF-G dissociation. | |||||||||||||||
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_25415.map.gz | 320.5 MB | EMDB map data format | |
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Header (meta data) | emd-25415-v30.xml emd-25415.xml | 77.2 KB 77.2 KB | Display Display | EMDB header |
Images | emd_25415.png | 201 KB | ||
Filedesc metadata | emd-25415.cif.gz | 13.4 KB | ||
Others | emd_25415_additional_1.map.gz emd_25415_half_map_1.map.gz emd_25415_half_map_2.map.gz | 317.5 MB 167.3 MB 167.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25415 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25415 | HTTPS FTP |
-Validation report
Summary document | emd_25415_validation.pdf.gz | 1005.1 KB | Display | EMDB validaton report |
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Full document | emd_25415_full_validation.pdf.gz | 1004.6 KB | Display | |
Data in XML | emd_25415_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | emd_25415_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25415 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25415 | HTTPS FTP |
-Related structure data
Related structure data | 7sswMC 7ss9C 7ssdC 7sslC 7ssnC 7ssoC 7st2C 7st6C 7st7C C: citing same article (ref.) M: atomic model generated by this map |
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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_25415.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | main map used in refinement; blocfiltered and sharpened to -50 at 3.8A | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8271 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: map of VI
File | emd_25415_additional_1.map | ||||||||||||
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Annotation | map of VI | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_25415_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_25415_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Late translocation intermediate with EF-G dissociated (Structure VI)
+Supramolecule #1: Late translocation intermediate with EF-G dissociated (Structure VI)
+Macromolecule #1: 16S rRNA
+Macromolecule #2: 23S rRNA
+Macromolecule #3: 5S rRNA
+Macromolecule #4: tRNA fMet
+Macromolecule #35: mRNA
+Macromolecule #36: tRNA Pro
+Macromolecule #5: 50S ribosomal protein L2
+Macromolecule #6: 50S ribosomal protein L3
+Macromolecule #7: 50S ribosomal protein L4
+Macromolecule #8: 50S ribosomal protein L5
+Macromolecule #9: 50S ribosomal protein L6
+Macromolecule #10: 50S ribosomal protein L9
+Macromolecule #11: 50S ribosomal protein L1
+Macromolecule #12: 50S ribosomal protein L11
+Macromolecule #13: 50S ribosomal protein L13
+Macromolecule #14: 50S ribosomal protein L14
+Macromolecule #15: 50S ribosomal protein L15
+Macromolecule #16: 50S ribosomal protein L16
+Macromolecule #17: 50S ribosomal protein L17
+Macromolecule #18: 50S ribosomal protein L18
+Macromolecule #19: 50S ribosomal protein L19
+Macromolecule #20: 50S ribosomal protein L20
+Macromolecule #21: 50S ribosomal protein L21
+Macromolecule #22: 50S ribosomal protein L22
+Macromolecule #23: 50S ribosomal protein L23
+Macromolecule #24: 50S ribosomal protein L24
+Macromolecule #25: 50S ribosomal protein L25
+Macromolecule #26: 50S ribosomal protein L27
+Macromolecule #27: 50S ribosomal protein L28
+Macromolecule #28: 50S ribosomal protein L29
+Macromolecule #29: 50S ribosomal protein L30
+Macromolecule #30: 50S ribosomal protein L32
+Macromolecule #31: 50S ribosomal protein L33
+Macromolecule #32: 50S ribosomal protein L34
+Macromolecule #33: 50S ribosomal protein L35
+Macromolecule #34: 50S ribosomal protein L36
+Macromolecule #37: 30S ribosomal protein S2
+Macromolecule #38: 30S ribosomal protein S3
+Macromolecule #39: 30S ribosomal protein S4
+Macromolecule #40: 30S ribosomal protein S5
+Macromolecule #41: 30S ribosomal protein S6
+Macromolecule #42: 30S ribosomal protein S7
+Macromolecule #43: 30S ribosomal protein S8
+Macromolecule #44: 30S ribosomal protein S9
+Macromolecule #45: 30S ribosomal protein S10
+Macromolecule #46: 30S ribosomal protein S11
+Macromolecule #47: 30S ribosomal protein S12
+Macromolecule #48: 30S ribosomal protein S13
+Macromolecule #49: 30S ribosomal protein S14
+Macromolecule #50: 30S ribosomal protein S15
+Macromolecule #51: 30S ribosomal protein S16
+Macromolecule #52: 30S ribosomal protein S17
+Macromolecule #53: 30S ribosomal protein S18
+Macromolecule #54: 30S ribosomal protein S19
+Macromolecule #55: 30S ribosomal protein S20
+Macromolecule #56: 30S ribosomal protein S21
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 47.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN / Number images used: 1163 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: FREALIGN |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: FREALIGN |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Output model | PDB-7ssw: |