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- EMDB-3489: Structure of ArfA and RF2 bound to the 70S ribosome (accommodated... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3489 | |||||||||
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Title | Structure of ArfA and RF2 bound to the 70S ribosome (accommodated state) | |||||||||
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![]() | ribosome ArfA RF2 trans-translation 70S 50S 30S rescue termination cryo-EM / ribosome | |||||||||
Function / homology | ![]() translation release factor activity, codon specific / negative regulation of cytoplasmic translational initiation / stringent response / ribosomal large subunit binding / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation ...translation release factor activity, codon specific / negative regulation of cytoplasmic translational initiation / stringent response / ribosomal large subunit binding / 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 / rescue of stalled ribosome / 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 / 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 / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.97 Å | |||||||||
![]() | James NR / Brown A | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Translational termination without a stop codon. Authors: Nathan R James / Alan Brown / Yuliya Gordiyenko / V Ramakrishnan / ![]() Abstract: Ribosomes stall when they encounter the end of messenger RNA (mRNA) without an in-frame stop codon. In bacteria, these "nonstop" complexes can be rescued by alternative ribosome-rescue factor A (ArfA) ...Ribosomes stall when they encounter the end of messenger RNA (mRNA) without an in-frame stop codon. In bacteria, these "nonstop" complexes can be rescued by alternative ribosome-rescue factor A (ArfA). We used electron cryomicroscopy to determine structures of ArfA bound to the ribosome with 3'-truncated mRNA, at resolutions ranging from 3.0 to 3.4 angstroms. ArfA binds within the ribosomal mRNA channel and substitutes for the absent stop codon in the A site by specifically recruiting release factor 2 (RF2), initially in a compact preaccommodated state. A similar conformation of RF2 may occur on stop codons, suggesting a general mechanism for release-factor-mediated translational termination in which a conformational switch leads to peptide release only when the appropriate signal is present in the A site. | |||||||||
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 | ![]() | 17.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 77 KB 77 KB | Display Display | ![]() |
Images | ![]() | 236.4 KB | ||
Filedesc metadata | ![]() | 15.2 KB | ||
Others | ![]() ![]() | 193.6 MB 193.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mdvMC ![]() 3490C ![]() 3492C ![]() 3493C ![]() 5mdwC ![]() 5mdyC ![]() 5mdzC 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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_3489_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_3489_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Structure of ArfA and RF2 bound to the 70S ribosome (accommodated...
+Supramolecule #1: Structure of ArfA and RF2 bound to the 70S ribosome (accommodated...
+Macromolecule #1: 23S ribosomal RNA
+Macromolecule #2: 16S ribosomal RNA
+Macromolecule #3: 5S ribosomal RNA
+Macromolecule #4: mRNA
+Macromolecule #5: fMet-NH-tRNA(fMet)
+Macromolecule #6: Alternative ribosome-rescue factor A
+Macromolecule #7: Peptide chain release factor 2
+Macromolecule #8: 50S ribosomal protein L2
+Macromolecule #9: 50S ribosomal protein L3
+Macromolecule #10: 50S ribosomal protein L4
+Macromolecule #11: 50S ribosomal protein L5
+Macromolecule #12: 50S ribosomal protein L6
+Macromolecule #13: 50S ribosomal protein L9
+Macromolecule #14: 50S ribosomal protein L10
+Macromolecule #15: 50S ribosomal protein L11
+Macromolecule #16: 50S ribosomal protein L13
+Macromolecule #17: 50S ribosomal protein L14
+Macromolecule #18: 50S ribosomal protein L15
+Macromolecule #19: 50S ribosomal protein L16
+Macromolecule #20: 50S ribosomal protein L17
+Macromolecule #21: 50S ribosomal protein L18
+Macromolecule #22: 50S ribosomal protein L19
+Macromolecule #23: 50S ribosomal protein L20
+Macromolecule #24: 50S ribosomal protein L21
+Macromolecule #25: 50S ribosomal protein L22
+Macromolecule #26: 50S ribosomal protein L23
+Macromolecule #27: 50S ribosomal protein L24
+Macromolecule #28: 50S ribosomal protein L25
+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: 30S ribosomal protein S2
+Macromolecule #40: 30S ribosomal protein S3
+Macromolecule #41: 30S ribosomal protein S4
+Macromolecule #42: 30S ribosomal protein S5
+Macromolecule #43: 30S ribosomal protein S6
+Macromolecule #44: 30S ribosomal protein S7
+Macromolecule #45: 30S ribosomal protein S8
+Macromolecule #46: 30S ribosomal protein S9
+Macromolecule #47: 30S ribosomal protein S10
+Macromolecule #48: 30S ribosomal protein S11
+Macromolecule #49: 30S ribosomal protein S12
+Macromolecule #50: 30S ribosomal protein S13
+Macromolecule #51: 30S ribosomal protein S14
+Macromolecule #52: 30S ribosomal protein S15
+Macromolecule #53: 30S ribosomal protein S16
+Macromolecule #54: 30S ribosomal protein S17
+Macromolecule #55: 30S ribosomal protein S18
+Macromolecule #56: 30S ribosomal protein S19
+Macromolecule #57: 30S ribosomal protein S20
+Macromolecule #58: 30S ribosomal protein S21
+Macromolecule #59: MAGNESIUM ION
+Macromolecule #60: N-FORMYLMETHIONINE
+Macromolecule #61: ZINC ION
+Macromolecule #62: water
-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: 7.4 Component:
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 6 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 1.2 sec. / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 134615 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 75.3 |
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Output model | ![]() PDB-5mdv: |