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- EMDB-25421: Pre translocation intermediate stalled with viomycin and bound wi... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-25421 | |||||||||||||||
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Title | Pre translocation intermediate stalled with viomycin and bound with EF-G in a GDP and Pi state (Structure III-vio) | |||||||||||||||
![]() | beamtilt corrected map used in refinement of III-vio | |||||||||||||||
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Function / homology | ![]() negative regulation of cytoplasmic translational initiation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() | |||||||||||||||
![]() | Carbone CE / Korostelev AA | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 317.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 75.1 KB 75.1 KB | Display Display | ![]() |
Images | ![]() | 104.6 KB | ||
Others | ![]() ![]() ![]() | 320.6 MB 144.1 MB 144.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7st7MC ![]() 7ss9C ![]() 7ssdC ![]() 7sslC ![]() 7ssnC ![]() 7ssoC ![]() 7sswC ![]() 7st2C ![]() 7st6C C: citing same article ( M: atomic model generated by this map |
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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 | beamtilt corrected map used in refinement of III-vio | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.87 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: beamtilt corrected map of III-vio that was blocfiltered...
File | emd_25421_additional_1.map | ||||||||||||
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Annotation | beamtilt corrected map of III-vio that was blocfiltered and sharpened to -50 at 3.2A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_25421_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_25421_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Pre translocation intermediate stalled with viomycin and bound wi...
+Supramolecule #1: Pre translocation intermediate stalled with viomycin and bound wi...
+Macromolecule #1: 23S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #41: 16S rRNA
+Macromolecule #42: mRNA
+Macromolecule #57: tRNA fMet
+Macromolecule #58: tRNA Pro
+Macromolecule #3: 50S ribosomal protein L2
+Macromolecule #4: 50S ribosomal protein L3
+Macromolecule #5: 50S ribosomal protein L4
+Macromolecule #6: 50S ribosomal protein L5
+Macromolecule #7: 50S ribosomal protein L6
+Macromolecule #8: 50S ribosomal protein L9
+Macromolecule #9: 50S ribosomal protein L1
+Macromolecule #10: 50S ribosomal protein L11
+Macromolecule #11: 50S ribosomal protein L13
+Macromolecule #12: 50S ribosomal protein L14
+Macromolecule #13: 50S ribosomal protein L15
+Macromolecule #14: 50S ribosomal protein L16
+Macromolecule #15: 50S ribosomal protein L17
+Macromolecule #16: 50S ribosomal protein L18
+Macromolecule #17: 50S ribosomal protein L19
+Macromolecule #18: 50S ribosomal protein L20
+Macromolecule #19: 50S ribosomal protein L21
+Macromolecule #20: 50S ribosomal protein L22
+Macromolecule #21: 50S ribosomal protein L23
+Macromolecule #22: 50S ribosomal protein L24
+Macromolecule #23: 50S ribosomal protein L25
+Macromolecule #24: 50S ribosomal protein L27
+Macromolecule #25: 50S ribosomal protein L28
+Macromolecule #26: 50S ribosomal protein L29
+Macromolecule #27: 50S ribosomal protein L30
+Macromolecule #28: 50S ribosomal protein L31
+Macromolecule #29: 50S ribosomal protein L32
+Macromolecule #30: 50S ribosomal protein L33
+Macromolecule #31: 50S ribosomal protein L34
+Macromolecule #32: 50S ribosomal protein L35
+Macromolecule #33: 50S ribosomal protein L36
+Macromolecule #34: 30S ribosomal protein S3
+Macromolecule #35: 30S ribosomal protein S7
+Macromolecule #36: 30S ribosomal protein S9
+Macromolecule #37: 30S ribosomal protein S10
+Macromolecule #38: 30S ribosomal protein S13
+Macromolecule #39: 30S ribosomal protein S14
+Macromolecule #40: 30S ribosomal protein S19
+Macromolecule #43: 30S ribosomal protein S2
+Macromolecule #44: 30S ribosomal protein S4
+Macromolecule #45: 30S ribosomal protein S5
+Macromolecule #46: 30S ribosomal protein S6
+Macromolecule #47: 30S ribosomal protein S8
+Macromolecule #48: 30S ribosomal protein S11
+Macromolecule #49: 30S ribosomal protein S12
+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 S20
+Macromolecule #55: 30S ribosomal protein S21
+Macromolecule #56: Elongation factor G
+Macromolecule #59: Viomycin
+Macromolecule #60: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #61: PHOSPHATE ION
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.5 e/Å2 |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
CTF correction | Software - Name: CTFFIND |
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Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: FREALIGN |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: FREALIGN |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN / Number images used: 20167 |