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Yorodumi- EMDB-4001: Cryo-EM structure of stringent response factor RelA bound to ErmC... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4001 | ||||||||||||||||||
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Title | Cryo-EM structure of stringent response factor RelA bound to ErmCL-stalled ribosome complex | ||||||||||||||||||
Map data | None | ||||||||||||||||||
Sample |
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Keywords | Stringent Response / RelA / Ribosome / Cryo-EM | ||||||||||||||||||
Function / homology | Function and homology information guanosine tetraphosphate metabolic process / GTP diphosphokinase activity / GTP diphosphokinase / guanosine tetraphosphate biosynthetic process / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / nucleobase-containing small molecule interconversion / negative regulation of cytoplasmic translational initiation / stringent response / response to starvation / ornithine decarboxylase inhibitor activity ...guanosine tetraphosphate metabolic process / GTP diphosphokinase activity / GTP diphosphokinase / guanosine tetraphosphate biosynthetic process / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / nucleobase-containing small molecule interconversion / negative regulation of cytoplasmic translational initiation / stringent response / response to starvation / 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 / 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 / kinase activity / 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 / GTP binding / DNA binding / RNA binding / zinc ion binding / ATP binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli K-12 (bacteria) / Escherichia coli K12 (bacteria) / Escherichia coli (strain K12) (bacteria) / Escherichia coli O157:H7 (bacteria) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||||||||
Authors | Arenz S / Wilson DN | ||||||||||||||||||
Funding support | Germany, Sweden, 5 items
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Citation | Journal: Nucleic Acids Res / Year: 2016 Title: The stringent factor RelA adopts an open conformation on the ribosome to stimulate ppGpp synthesis. Authors: Stefan Arenz / Maha Abdelshahid / Daniel Sohmen / Roshani Payoe / Agata L Starosta / Otto Berninghausen / Vasili Hauryliuk / Roland Beckmann / Daniel N Wilson / Abstract: Under stress conditions, such as nutrient starvation, deacylated tRNAs bound within the ribosomal A-site are recognized by the stringent factor RelA, which converts ATP and GTP/GDP to (p)ppGpp. The ...Under stress conditions, such as nutrient starvation, deacylated tRNAs bound within the ribosomal A-site are recognized by the stringent factor RelA, which converts ATP and GTP/GDP to (p)ppGpp. The signaling molecules (p)ppGpp globally rewire the cellular transcriptional program and general metabolism, leading to stress adaptation. Despite the additional importance of the stringent response for regulation of bacterial virulence, antibiotic resistance and persistence, structural insight into how the ribosome and deacylated-tRNA stimulate RelA-mediated (p)ppGpp has been lacking. Here, we present a cryo-EM structure of RelA in complex with the Escherichia coli 70S ribosome with an average resolution of 3.7 Å and local resolution of 4 to >10 Å for RelA. The structure reveals that RelA adopts a unique 'open' conformation, where the C-terminal domain (CTD) is intertwined around an A/T-like tRNA within the intersubunit cavity of the ribosome and the N-terminal domain (NTD) extends into the solvent. We propose that the open conformation of RelA on the ribosome relieves the autoinhibitory effect of the CTD on the NTD, thus leading to stimulation of (p)ppGpp synthesis by RelA. | ||||||||||||||||||
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_4001.map.gz | 177.5 MB | EMDB map data format | |
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Header (meta data) | emd-4001-v30.xml emd-4001.xml | 73.4 KB 73.4 KB | Display Display | EMDB header |
Images | emd_4001.png | 33.5 KB | ||
Filedesc metadata | emd-4001.cif.gz | 14.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4001 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4001 | HTTPS FTP |
-Validation report
Summary document | emd_4001_validation.pdf.gz | 616.2 KB | Display | EMDB validaton report |
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Full document | emd_4001_full_validation.pdf.gz | 615.8 KB | Display | |
Data in XML | emd_4001_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | emd_4001_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4001 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4001 | HTTPS FTP |
-Related structure data
Related structure data | 5l3pMC 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_4001.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 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 : Cryo-EM structure of stringent response factor RelA bound to ErmC...
+Supramolecule #1: Cryo-EM structure of stringent response factor RelA bound to ErmC...
+Macromolecule #1: 23S ribosomal RNA
+Macromolecule #2: 5S ribosomal RNA
+Macromolecule #32: 16S ribosomal RNA
+Macromolecule #51: mRNA
+Macromolecule #52: P-site tRNA
+Macromolecule #58: deacylated A/R-tRNA
+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 S15
+Macromolecule #46: 30S ribosomal protein S16
+Macromolecule #47: 30S ribosomal protein S17
+Macromolecule #48: 30S ribosomal protein S18
+Macromolecule #49: 30S ribosomal protein S20
+Macromolecule #50: 30S ribosomal protein S21
+Macromolecule #53: 50S ribosomal protein L10
+Macromolecule #54: 50S ribosomal protein L11
+Macromolecule #55: 30S ribosomal protein S14
+Macromolecule #56: 30S ribosomal protein S19
+Macromolecule #57: GTP pyrophosphokinase,GTP pyrophosphokinase,GTP pyrophosphokinase
-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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Grid | Model: Quantifoil R3/3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY |
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) / Detector mode: INTEGRATING / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPIDER / Number images used: 24749 |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: SPIDER |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: SPIDER |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-5l3p: |