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- EMDB-21625: Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA pro... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21625 | ||||||||||||
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Title | Cryo-EM of elongating ribosome with EF-Tu*GTP elucidates tRNA proofreading (Cognate Structure II-C2) | ||||||||||||
![]() | Map II-C2 blocfilt filtered and with B-factor -50 applied | ||||||||||||
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![]() | Ribosome / EF-Tu / tRNA | ||||||||||||
Function / homology | ![]() guanosine tetraphosphate binding / 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 ...guanosine tetraphosphate binding / 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 / translation elongation factor activity / translational termination / DnaA-L2 complex / four-way junction DNA binding / 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 / transcription antitermination / response to reactive oxygen species / regulation of cell growth / ribosomal large subunit assembly / 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 / GTPase activity / negative regulation of DNA-templated transcription / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / membrane / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
![]() | Loveland AB / Demo G | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM of elongating ribosome with EF-Tu•GTP elucidates tRNA proofreading. Authors: Anna B Loveland / Gabriel Demo / Andrei A Korostelev / ![]() ![]() Abstract: Ribosomes accurately decode mRNA by proofreading each aminoacyl-tRNA that is delivered by the elongation factor EF-Tu. To understand the molecular mechanism of this proofreading step it is necessary ...Ribosomes accurately decode mRNA by proofreading each aminoacyl-tRNA that is delivered by the elongation factor EF-Tu. To understand the molecular mechanism of this proofreading step it is necessary to visualize GTP-catalysed elongation, which has remained a challenge. Here we use time-resolved cryogenic electron microscopy to reveal 33 ribosomal states after the delivery of aminoacyl-tRNA by EF-Tu•GTP. Instead of locking cognate tRNA upon initial recognition, the ribosomal decoding centre dynamically monitors codon-anticodon interactions before and after GTP hydrolysis. GTP hydrolysis enables the GTPase domain of EF-Tu to extend away, releasing EF-Tu from tRNA. The 30S subunit then locks cognate tRNA in the decoding centre and rotates, enabling the tRNA to bypass 50S protrusions during accommodation into the peptidyl transferase centre. By contrast, the decoding centre fails to lock near-cognate tRNA, enabling the dissociation of near-cognate tRNA both during initial selection (before GTP hydrolysis) and proofreading (after GTP hydrolysis). These findings reveal structural similarity between ribosomes in initial selection states and in proofreading states, which together govern the efficient rejection of incorrect tRNA. | ||||||||||||
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 | ![]() | 85.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 79.8 KB 79.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.9 KB | Display | ![]() |
Images | ![]() | 130.4 KB | ||
Filedesc metadata | ![]() | 14.1 KB | ||
Others | ![]() ![]() ![]() | 84.5 MB 34 MB 34 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wd6MC ![]() 6wd0C ![]() 6wd1C ![]() 6wd2C ![]() 6wd3C ![]() 6wd4C ![]() 6wd5C ![]() 6wd7C ![]() 6wd8C ![]() 6wd9C ![]() 6wdaC ![]() 6wdbC ![]() 6wdcC ![]() 6wddC ![]() 6wdeC ![]() 6wdfC ![]() 6wdgC ![]() 6wdhC ![]() 6wdiC ![]() 6wdjC ![]() 6wdkC ![]() 6wdlC ![]() 6wdmC 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
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Annotation | Map II-C2 blocfilt filtered and with B-factor -50 applied | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.333 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 II-C2
File | emd_21625_additional.map | ||||||||||||
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Annotation | Map II-C2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 II-C2
File | emd_21625_half_map_1.map | ||||||||||||
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Annotation | Half map 1 II-C2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 II-C2
File | emd_21625_half_map_2.map | ||||||||||||
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Annotation | Half map 2 II-C2 | ||||||||||||
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Density Histograms |
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Sample components
+Entire : Map II-C2
+Supramolecule #1: Map II-C2
+Macromolecule #1: 50S ribosomal protein L2
+Macromolecule #2: 50S ribosomal protein L3
+Macromolecule #3: 50S ribosomal protein L4
+Macromolecule #4: 50S ribosomal protein L5
+Macromolecule #5: 50S ribosomal protein L6
+Macromolecule #6: 50S ribosomal protein L9
+Macromolecule #7: 50S ribosomal protein L10
+Macromolecule #8: 50S ribosomal protein L11
+Macromolecule #9: 50S ribosomal protein L13
+Macromolecule #10: 50S ribosomal protein L14
+Macromolecule #11: 50S ribosomal protein L15
+Macromolecule #12: 50S ribosomal protein L16
+Macromolecule #13: 50S ribosomal protein L17
+Macromolecule #14: 50S ribosomal protein L18
+Macromolecule #15: 50S ribosomal protein L19
+Macromolecule #16: 50S ribosomal protein L20
+Macromolecule #17: 50S ribosomal protein L21
+Macromolecule #18: 50S ribosomal protein L22
+Macromolecule #19: 50S ribosomal protein L23
+Macromolecule #20: 50S ribosomal protein L24
+Macromolecule #21: 50S ribosomal protein L25
+Macromolecule #22: 50S ribosomal protein L27
+Macromolecule #23: 50S ribosomal protein L28
+Macromolecule #24: 50S ribosomal protein L29
+Macromolecule #25: 50S ribosomal protein L30
+Macromolecule #26: 50S ribosomal protein L32
+Macromolecule #27: 50S ribosomal protein L33
+Macromolecule #28: 50S ribosomal protein L34
+Macromolecule #29: 50S ribosomal protein L35
+Macromolecule #30: 50S ribosomal protein L36
+Macromolecule #31: 30S ribosomal protein S2
+Macromolecule #32: 30S ribosomal protein S3
+Macromolecule #33: 30S ribosomal protein S4
+Macromolecule #34: 30S ribosomal protein S5
+Macromolecule #35: 30S ribosomal protein S6
+Macromolecule #36: 30S ribosomal protein S7
+Macromolecule #37: 30S ribosomal protein S8
+Macromolecule #38: 30S ribosomal protein S9
+Macromolecule #39: 30S ribosomal protein S10
+Macromolecule #40: 30S ribosomal protein S11
+Macromolecule #41: 30S ribosomal protein S12
+Macromolecule #42: 30S ribosomal protein S13
+Macromolecule #43: 30S ribosomal protein S14
+Macromolecule #44: 30S ribosomal protein S15
+Macromolecule #45: 30S ribosomal protein S16
+Macromolecule #46: 30S ribosomal protein S17
+Macromolecule #47: 30S ribosomal protein S18
+Macromolecule #48: 30S ribosomal protein S19
+Macromolecule #49: 30S ribosomal protein S20
+Macromolecule #50: 30S ribosomal protein S21
+Macromolecule #51: 50S ribosomal protein L1
+Macromolecule #58: Elongation factor Tu
+Macromolecule #52: 16S ribosomal RNA
+Macromolecule #53: 23S ribosomal RNA
+Macromolecule #54: 5S ribosomal RNA
+Macromolecule #55: tRNAfMet
+Macromolecule #56: mRNA
+Macromolecule #57: tRNAPhe
+Macromolecule #59: N-FORMYLMETHIONINE
+Macromolecule #60: PHENYLALANINE
+Macromolecule #61: GUANOSINE-5'-DIPHOSPHATE
-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: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-35 / Number grids imaged: 1 / Number real images: 3218 / Average exposure time: 1.0 sec. / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient |
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Output model | ![]() PDB-6wd6: |