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Yorodumi- EMDB-3898: Cryo-EM structure of a polyproline-stalled ribosome in the absenc... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3898 | |||||||||
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Title | Cryo-EM structure of a polyproline-stalled ribosome in the absence of EF-P | |||||||||
Map data | Polyproline stalled ribosome with P-tRNA. This volume derives from polyproline stalled ribosomes that were incubated together with elongation-factor P (EF-P) | |||||||||
Sample |
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Function / homology | Function and homology information negative regulation of cytoplasmic translational initiation / 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 translational initiation / 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 / 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 / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / DNA endonuclease activity / 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 / ribosomal small subunit biogenesis / large ribosomal subunit / ribosome biogenesis / small ribosomal subunit rRNA binding / ribosome binding / ribosomal large subunit assembly / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / molecular adaptor activity / negative regulation of translation / rRNA binding / 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 | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Huter P / Arenz S / Wilson DN | |||||||||
Citation | Journal: Mol Cell / Year: 2017 Title: Structural Basis for Polyproline-Mediated Ribosome Stalling and Rescue by the Translation Elongation Factor EF-P. Authors: Paul Huter / Stefan Arenz / Lars V Bock / Michael Graf / Jan Ole Frister / Andre Heuer / Lauri Peil / Agata L Starosta / Ingo Wohlgemuth / Frank Peske / Jiří Nováček / Otto Berninghausen ...Authors: Paul Huter / Stefan Arenz / Lars V Bock / Michael Graf / Jan Ole Frister / Andre Heuer / Lauri Peil / Agata L Starosta / Ingo Wohlgemuth / Frank Peske / Jiří Nováček / Otto Berninghausen / Helmut Grubmüller / Tanel Tenson / Roland Beckmann / Marina V Rodnina / Andrea C Vaiana / Daniel N Wilson / Abstract: Ribosomes synthesizing proteins containing consecutive proline residues become stalled and require rescue via the action of uniquely modified translation elongation factors, EF-P in bacteria, or ...Ribosomes synthesizing proteins containing consecutive proline residues become stalled and require rescue via the action of uniquely modified translation elongation factors, EF-P in bacteria, or archaeal/eukaryotic a/eIF5A. To date, no structures exist of EF-P or eIF5A in complex with translating ribosomes stalled at polyproline stretches, and thus structural insight into how EF-P/eIF5A rescue these arrested ribosomes has been lacking. Here we present cryo-EM structures of ribosomes stalled on proline stretches, without and with modified EF-P. The structures suggest that the favored conformation of the polyproline-containing nascent chain is incompatible with the peptide exit tunnel of the ribosome and leads to destabilization of the peptidyl-tRNA. Binding of EF-P stabilizes the P-site tRNA, particularly via interactions between its modification and the CCA end, thereby enforcing an alternative conformation of the polyproline-containing nascent chain, which allows a favorable substrate geometry for peptide bond formation. | |||||||||
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_3898.map.gz | 20.7 MB | EMDB map data format | |
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Header (meta data) | emd-3898-v30.xml emd-3898.xml | 60.9 KB 60.9 KB | Display Display | EMDB header |
Images | emd_3898.png | 71.9 KB | ||
Others | emd_3898_additional.map.gz | 15.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3898 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3898 | HTTPS FTP |
-Validation report
Summary document | emd_3898_validation.pdf.gz | 258.5 KB | Display | EMDB validaton report |
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Full document | emd_3898_full_validation.pdf.gz | 257.6 KB | Display | |
Data in XML | emd_3898_validation.xml.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3898 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3898 | HTTPS FTP |
-Related structure data
Related structure data | 6enfMC 3899C 3900C 3901C 3902C 3903C 6enjC 6enuC M: atomic model generated by this map C: citing same article (ref.) |
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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_3898.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Polyproline stalled ribosome with P-tRNA. This volume derives from polyproline stalled ribosomes that were incubated together with elongation-factor P (EF-P) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: None
File | emd_3898_additional.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Polyproline stalled ribosome in the absence of elongation factor P
+Supramolecule #1: Polyproline stalled ribosome in the absence of elongation factor P
+Macromolecule #1: 16S ribosomal RNA
+Macromolecule #22: RNA (5'-R(P*CP*CP*G)-3'), mRNA
+Macromolecule #23: 23S ribosomal RNA
+Macromolecule #24: 5S ribosomal RNA
+Macromolecule #53: proline 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 L13
+Macromolecule #31: 50S ribosomal protein L14
+Macromolecule #32: 50S ribosomal protein L15
+Macromolecule #33: 50S ribosomal protein L16
+Macromolecule #34: 50S ribosomal protein L17
+Macromolecule #35: 50S ribosomal protein L18
+Macromolecule #36: 50S ribosomal protein L19
+Macromolecule #37: 50S ribosomal protein L20
+Macromolecule #38: 50S ribosomal protein L21
+Macromolecule #39: 50S ribosomal protein L22
+Macromolecule #40: 50S ribosomal protein L23
+Macromolecule #41: 50S ribosomal protein L24
+Macromolecule #42: 50S ribosomal protein L25
+Macromolecule #43: 50S ribosomal protein L27
+Macromolecule #44: 50S ribosomal protein L28
+Macromolecule #45: 50S ribosomal protein L29
+Macromolecule #46: 50S ribosomal protein L30
+Macromolecule #47: 50S ribosomal protein L32
+Macromolecule #48: 50S ribosomal protein L33
+Macromolecule #49: 50S ribosomal protein L34
+Macromolecule #50: 50S ribosomal protein L35
+Macromolecule #51: 50S ribosomal protein L36
+Macromolecule #52: 50S ribosomal protein L31
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 28.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75089 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-6enf: |