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Yorodumi- EMDB-8597: 70S ribosome complex with dnaX mRNA stem-loop and E-site tRNA ("o... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8597 | |||||||||
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Title | 70S ribosome complex with dnaX mRNA stem-loop and E-site tRNA ("out" conformation) | |||||||||
Map data | 70S ribosome complex with dnaX mRNA stem-loop and E-site tRNA ("out" conformation) | |||||||||
Sample |
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Function / homology | Function and homology information large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit ...large ribosomal subunit / regulation of translation / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) / Escherichia coli K-12 (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Zhang Y / Hong S / Skiniotis G / Dunham CM | |||||||||
Citation | Journal: Structure / Year: 2018 Title: Alternative Mode of E-Site tRNA Binding in the Presence of a Downstream mRNA Stem Loop at the Entrance Channel. Authors: Yan Zhang / Samuel Hong / Ajchareeya Ruangprasert / Georgios Skiniotis / Christine M Dunham / Abstract: Structured mRNAs positioned downstream of the ribosomal decoding center alter gene expression by slowing protein synthesis. Here, we solved the cryo-EM structure of the bacterial ribosome bound to an ...Structured mRNAs positioned downstream of the ribosomal decoding center alter gene expression by slowing protein synthesis. Here, we solved the cryo-EM structure of the bacterial ribosome bound to an mRNA containing a 3' stem loop that regulates translation. Unexpectedly, the E-site tRNA adopts two distinct orientations. In the first structure, normal interactions with the 50S and 30S E site are observed. However, in the second structure, although the E-site tRNA makes normal interactions with the 50S E site, its anticodon stem loop moves ∼54 Å away from the 30S E site to interact with the 30S head domain and 50S uL5. This position of the E-site tRNA causes the uL1 stalk to adopt a more open conformation that likely represents an intermediate state during E-site tRNA dissociation. These results suggest that structured mRNAs at the entrance channel restrict 30S subunit movement required during translation to slow E-site tRNA dissociation. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8597.map.gz | 201.5 MB | EMDB map data format | |
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Header (meta data) | emd-8597-v30.xml emd-8597.xml | 67 KB 67 KB | Display Display | EMDB header |
Images | emd_8597.png | 195.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8597 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8597 | HTTPS FTP |
-Validation report
Summary document | emd_8597_validation.pdf.gz | 594.1 KB | Display | EMDB validaton report |
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Full document | emd_8597_full_validation.pdf.gz | 593.7 KB | Display | |
Data in XML | emd_8597_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_8597_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8597 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8597 | HTTPS FTP |
-Related structure data
Related structure data | 5uq8MC 8596C 5uq7C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8597.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 70S ribosome complex with dnaX mRNA stem-loop and E-site tRNA ("out" conformation) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : 70S-dnaX complex
+Supramolecule #1: 70S-dnaX complex
+Macromolecule #1: 23S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #32: 16S rRNA
+Macromolecule #53: P-site tRNA fMet
+Macromolecule #55: E-site tRNA Phe
+Macromolecule #56: messenger RNA
+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 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 L31
+Macromolecule #27: 50S ribosomal protein L32
+Macromolecule #28: 50S ribosomal protein L33
+Macromolecule #29: 50S ribosomal protein L34
+Macromolecule #30: 50S ribosomal protein L35
+Macromolecule #31: 50S ribosomal protein L36
+Macromolecule #33: 30S ribosomal protein S2
+Macromolecule #34: 30S ribosomal protein S3
+Macromolecule #35: 30S ribosomal protein S4
+Macromolecule #36: 30S ribosomal protein S5
+Macromolecule #37: 30S ribosomal protein S6
+Macromolecule #38: 30S ribosomal protein S7
+Macromolecule #39: 30S ribosomal protein S8
+Macromolecule #40: 30S ribosomal protein S9
+Macromolecule #41: 30S ribosomal protein S10
+Macromolecule #42: 30S ribosomal protein S11
+Macromolecule #43: 30S ribosomal protein S12
+Macromolecule #44: 30S ribosomal protein S13
+Macromolecule #45: 30S ribosomal protein S14 type Z
+Macromolecule #46: 30S ribosomal protein S15
+Macromolecule #47: 30S ribosomal protein S16
+Macromolecule #48: 30S ribosomal protein S17
+Macromolecule #49: 30S ribosomal protein S18
+Macromolecule #50: 30S ribosomal protein S19
+Macromolecule #51: 30S ribosomal protein S20
+Macromolecule #52: 30S ribosomal protein Thx
+Macromolecule #54: 50S ribosomal protein L1
+Macromolecule #57: ZINC ION
+Macromolecule #58: IRON/SULFUR CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36361 |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-5uq8: |