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- EMDB-24134: Elongating 70S ribosome complex in a spectinomycin-stalled interm... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-24134 | |||||||||
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Title | Elongating 70S ribosome complex in a spectinomycin-stalled intermediate state of translocation bound to EF-G in an active, GTP conformation (INT1) | |||||||||
![]() | Post-processed map | |||||||||
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Function / homology | ![]() negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translation elongation factor activity ...negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translation elongation factor activity / 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 / 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 / translational initiation / 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 / GTPase activity / negative regulation of DNA-templated transcription / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.54 Å | |||||||||
![]() | Rundlet EJ / Holm M / Schacherl M / Natchiar KS / Altman RB / Spahn CMT / Myasnikov AG / Blanchard SC | |||||||||
![]() | ![]() Title: Structural basis of early translocation events on the ribosome. Authors: Emily J Rundlet / Mikael Holm / Magdalena Schacherl / S Kundhavai Natchiar / Roger B Altman / Christian M T Spahn / Alexander G Myasnikov / Scott C Blanchard / ![]() ![]() Abstract: Peptide-chain elongation during protein synthesis entails sequential aminoacyl-tRNA selection and translocation reactions that proceed rapidly (2-20 per second) and with a low error rate (around ...Peptide-chain elongation during protein synthesis entails sequential aminoacyl-tRNA selection and translocation reactions that proceed rapidly (2-20 per second) and with a low error rate (around 10 to 10 at each step) over thousands of cycles. The cadence and fidelity of ribosome transit through mRNA templates in discrete codon increments is a paradigm for movement in biological systems that must hold for diverse mRNA and tRNA substrates across domains of life. Here we use single-molecule fluorescence methods to guide the capture of structures of early translocation events on the bacterial ribosome. Our findings reveal that the bacterial GTPase elongation factor G specifically engages spontaneously achieved ribosome conformations while in an active, GTP-bound conformation to unlock and initiate peptidyl-tRNA translocation. These findings suggest that processes intrinsic to the pre-translocation ribosome complex can regulate the rate of protein synthesis, and that energy expenditure is used later in the translocation mechanism than previously proposed. | |||||||||
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 | ![]() | 16.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 80.1 KB 80.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.1 KB | Display | ![]() |
Images | ![]() | 61.3 KB | ||
Others | ![]() ![]() ![]() | 218.6 MB 411.4 MB 410.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7n2vMC ![]() 7n1pC ![]() 7n2cC ![]() 7n2uC ![]() 7n30C ![]() 7n31C 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 | Post-processed map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Masked refinement map
File | emd_24134_additional_1.map | ||||||||||||
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Annotation | Masked refinement map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map
File | emd_24134_half_map_1.map | ||||||||||||
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Annotation | Half map | ||||||||||||
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Density Histograms |
-Half map: Half map
File | emd_24134_half_map_2.map | ||||||||||||
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Annotation | Half map | ||||||||||||
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Density Histograms |
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Sample components
+Entire : Elongating 70S ribosome complex in a spectinomycin-stalled interm...
+Supramolecule #1: Elongating 70S ribosome complex in a spectinomycin-stalled interm...
+Macromolecule #1: 16S rRNA
+Macromolecule #22: mRNA
+Macromolecule #23: 23S rRNA
+Macromolecule #24: 5S rRNA
+Macromolecule #58: tRNA
+Macromolecule #59: tRNA
+Macromolecule #2: 30S ribosomal protein S2
+Macromolecule #3: 30S ribosomal protein S3
+Macromolecule #4: 30S ribosomal protein S4
+Macromolecule #5: 30S ribosomal protein S5
+Macromolecule #6: 30S ribosomal protein S6
+Macromolecule #7: 30S ribosomal protein S7
+Macromolecule #8: 30S ribosomal protein S8
+Macromolecule #9: 30S ribosomal protein S9
+Macromolecule #10: 30S ribosomal protein S10
+Macromolecule #11: 30S ribosomal protein S11
+Macromolecule #12: 30S ribosomal protein S12
+Macromolecule #13: 30S ribosomal protein S13
+Macromolecule #14: 30S ribosomal protein S14
+Macromolecule #15: 30S ribosomal protein S15
+Macromolecule #16: 30S ribosomal protein S16
+Macromolecule #17: 30S ribosomal protein S17
+Macromolecule #18: 30S ribosomal protein S18
+Macromolecule #19: 30S ribosomal protein S19
+Macromolecule #20: 30S ribosomal protein S20
+Macromolecule #21: 30S ribosomal protein S21
+Macromolecule #25: 50S ribosomal protein L2
+Macromolecule #26: 50S ribosomal protein L3
+Macromolecule #27: 50S ribosomal protein L4
+Macromolecule #28: 50S ribosomal protein L5
+Macromolecule #29: 50S ribosomal protein L6
+Macromolecule #30: 50S ribosomal protein L9
+Macromolecule #31: 50S ribosomal protein L10
+Macromolecule #32: 50S ribosomal protein L11
+Macromolecule #33: 50S ribosomal protein L13
+Macromolecule #34: 50S ribosomal protein L14
+Macromolecule #35: 50S ribosomal protein L15
+Macromolecule #36: 50S ribosomal protein L16
+Macromolecule #37: 50S ribosomal protein L17
+Macromolecule #38: 50S ribosomal protein L18
+Macromolecule #39: 50S ribosomal protein L19
+Macromolecule #40: 50S ribosomal protein L20
+Macromolecule #41: 50S ribosomal protein L21
+Macromolecule #42: 50S ribosomal protein L22
+Macromolecule #43: 50S ribosomal protein L23
+Macromolecule #44: 50S ribosomal protein L24
+Macromolecule #45: 50S ribosomal protein L25
+Macromolecule #46: 50S ribosomal protein L27
+Macromolecule #47: 50S ribosomal protein L28
+Macromolecule #48: 50S ribosomal protein L29
+Macromolecule #49: 50S ribosomal protein L30
+Macromolecule #50: 50S ribosomal protein L31
+Macromolecule #51: 50S ribosomal protein L32
+Macromolecule #52: 50S ribosomal protein L33
+Macromolecule #53: 50S ribosomal protein L34
+Macromolecule #54: 50S ribosomal protein L35
+Macromolecule #55: 50S ribosomal protein L36
+Macromolecule #56: Elongation factor G
+Macromolecule #57: Nascent peptide
+Macromolecule #60: SPECTINOMYCIN
+Macromolecule #61: 1,4-DIAMINOBUTANE
+Macromolecule #62: MAGNESIUM ION
+Macromolecule #63: ZINC ION
+Macromolecule #64: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #65: SPERMIDINE
+Macromolecule #66: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #67: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 5.5 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 87.0 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: RECIPROCAL / Protocol: OTHER |
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Output model | ![]() PDB-7n2v: |