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- EMDB-29624: Cryo-EM structure of an E. coli rotated ribosome complex bound wi... -
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Open data
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Basic information
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Title | Cryo-EM structure of an E. coli rotated ribosome complex bound with RF3-ppGpp and p/E-tRNAPhe (Composite state I-C) | ||||||||||||
![]() | Cryo-EM structure of an E. coli rotated ribosome complex bound with RF3-ppGpp and p/E-tRNAPhe (Composite state I-C) | ||||||||||||
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![]() | release factor 3 / termination complex / cryo-EM / tRNA / RIBOSOME / RIBOSOME-RNA complex | ||||||||||||
Function / homology | ![]() regulation of translational termination / translation release factor activity, codon nonspecific / translation release factor activity, codon specific / negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / positive regulation of ribosome biogenesis / translational termination / DnaA-L2 complex / negative regulation of translational initiation ...regulation of translational termination / translation release factor activity, codon nonspecific / translation release factor activity, codon specific / negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / positive regulation of ribosome biogenesis / translational termination / DnaA-L2 complex / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / translational initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / transcription antitermination / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit / GDP binding / ribosome binding / 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 / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / GTPase activity / mRNA binding / GTP binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
![]() | Rybak MY / Li L / Lin J / Gagnon MG | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: The ribosome termination complex remodels release factor RF3 and ejects GDP Authors: Li L / Rybak MY / Lin J / Gagnon MG | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 455.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 78.8 KB 78.8 KB | Display Display | ![]() |
Images | ![]() | 154 KB | ||
Filedesc metadata | ![]() | 16 KB | ||
Others | ![]() ![]() | 455.2 MB 455.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8fzfMC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 | Cryo-EM structure of an E. coli rotated ribosome complex bound with RF3-ppGpp and p/E-tRNAPhe (Composite state I-C) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Cryo-EM structure of an E. coli rotated ribosome...
File | emd_29624_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM structure of an E. coli rotated ribosome complex bound with RF3-ppGpp and p/E-tRNAPhe (Composite state I-C). Half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM structure of an E. coli rotated ribosome...
File | emd_29624_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM structure of an E. coli rotated ribosome complex bound with RF3-ppGpp and p/E-tRNAPhe (Composite state I-C). Half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Cryo-EM structure of an E. coli rotated ribosome complex bound wi...
+Supramolecule #1: Cryo-EM structure of an E. coli rotated ribosome complex bound wi...
+Macromolecule #1: 16S Ribosomal RNA
+Macromolecule #22: p/E phenylalanyl-tRNA
+Macromolecule #23: F-UAA mRNA
+Macromolecule #25: 23S Ribosomal RNA
+Macromolecule #26: 5S Ribosomal RNA
+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: Small ribosomal subunit protein uS9
+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: Small ribosomal subunit protein uS14
+Macromolecule #15: Small ribosomal subunit protein uS15
+Macromolecule #16: 30S ribosomal protein S16
+Macromolecule #17: Small ribosomal subunit protein uS17
+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 #24: Peptide chain release factor RF3
+Macromolecule #27: 50S ribosomal protein L2
+Macromolecule #28: 50S ribosomal protein L3
+Macromolecule #29: 50S ribosomal protein L4
+Macromolecule #30: 50S ribosomal protein L5
+Macromolecule #31: 50S ribosomal protein L6
+Macromolecule #32: 50S ribosomal protein L10
+Macromolecule #33: 50S ribosomal protein L11
+Macromolecule #34: 50S ribosomal protein L13
+Macromolecule #35: 50S ribosomal protein L14
+Macromolecule #36: 50S ribosomal protein L15
+Macromolecule #37: 50S ribosomal protein L16
+Macromolecule #38: Large ribosomal subunit protein bL17
+Macromolecule #39: 50S ribosomal protein L18
+Macromolecule #40: 50S ribosomal protein L19
+Macromolecule #41: 50S ribosomal protein L20
+Macromolecule #42: Ribosomal protein L21
+Macromolecule #43: 50S ribosomal protein L22
+Macromolecule #44: 50S ribosomal protein L23
+Macromolecule #45: 50S ribosomal protein L24
+Macromolecule #46: 50S ribosomal protein L25
+Macromolecule #47: 50S ribosomal protein L27
+Macromolecule #48: 50S ribosomal protein L28
+Macromolecule #49: 50S ribosomal protein L29
+Macromolecule #50: Large ribosomal subunit protein uL30
+Macromolecule #51: 50S ribosomal protein L31
+Macromolecule #52: 50S ribosomal protein L32
+Macromolecule #53: Large ribosomal subunit protein bL33
+Macromolecule #54: 50S ribosomal protein L34
+Macromolecule #55: 50S ribosomal protein L35
+Macromolecule #56: 50S ribosomal protein L36
+Macromolecule #57: MAGNESIUM ION
+Macromolecule #58: GUANOSINE-5',3'-TETRAPHOSPHATE
+Macromolecule #59: ZINC ION
+Macromolecule #60: 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 Details: 5 mM Tris-HCl, 60 mM NH4Cl, 10 mM MgCl2, 6 mM B-mercaptoethanol |
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 295 K / Instrument: LEICA EM GP |
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Electron microscopy
Microscope | TFS KRIOS |
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Software | Name: EPU (ver. 2.11.1) |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 10284 / Average exposure time: 1.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 96000 |
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
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Software | Name: ![]() |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-8fzf: |