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Yorodumi- EMDB-20416: Cryo-EM structure of the full-length Bacillus subtilis glyQS T-bo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20416 | |||||||||
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Title | Cryo-EM structure of the full-length Bacillus subtilis glyQS T-box riboswitch in complex with tRNA-Gly | |||||||||
Map data | T leader complex | |||||||||
Sample |
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Keywords | RNA complex / riboswitch / transcription attenuation / stacking. / RNA | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 Å | |||||||||
Authors | Li S / Su Z | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions. Authors: Shuang Li / Zhaoming Su / Jean Lehmann / Vassiliki Stamatopoulou / Nikoleta Giarimoglou / Frances E Henderson / Lixin Fan / Grigore D Pintilie / Kaiming Zhang / Muyuan Chen / Steven J Ludtke ...Authors: Shuang Li / Zhaoming Su / Jean Lehmann / Vassiliki Stamatopoulou / Nikoleta Giarimoglou / Frances E Henderson / Lixin Fan / Grigore D Pintilie / Kaiming Zhang / Muyuan Chen / Steven J Ludtke / Yun-Xing Wang / Constantinos Stathopoulos / Wah Chiu / Jinwei Zhang / Abstract: Amino acid availability in Gram-positive bacteria is monitored by T-box riboswitches. T-boxes directly bind tRNAs, assess their aminoacylation state, and regulate the transcription or translation of ...Amino acid availability in Gram-positive bacteria is monitored by T-box riboswitches. T-boxes directly bind tRNAs, assess their aminoacylation state, and regulate the transcription or translation of downstream genes to maintain nutritional homeostasis. Here, we report cocrystal and cryo-EM structures of Geobacillus kaustophilus and Bacillus subtilis T-box-tRNA complexes, detailing their multivalent, exquisitely selective interactions. The T-box forms a U-shaped molecular vise that clamps the tRNA, captures its 3' end using an elaborate 'discriminator' structure, and interrogates its aminoacylation state using a steric filter fashioned from a wobble base pair. In the absence of aminoacylation, T-boxes clutch tRNAs and form a continuously stacked central spine, permitting transcriptional readthrough or translation initiation. A modeled aminoacyl disrupts tRNA-T-box stacking, severing the central spine and blocking gene expression. Our data establish a universal mechanism of amino acid sensing on tRNAs and gene regulation by T-box riboswitches and exemplify how higher-order RNA-RNA interactions achieve multivalency and specificity. | |||||||||
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_20416.map.gz | 5.4 MB | EMDB map data format | |
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Header (meta data) | emd-20416-v30.xml emd-20416.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20416_fsc.xml | 8.1 KB | Display | FSC data file |
Images | emd_20416.png | 42.9 KB | ||
Masks | emd_20416_msk_1.map | 42.9 MB | Mask map | |
Filedesc metadata | emd-20416.cif.gz | 5.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20416 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20416 | HTTPS FTP |
-Validation report
Summary document | emd_20416_validation.pdf.gz | 412.1 KB | Display | EMDB validaton report |
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Full document | emd_20416_full_validation.pdf.gz | 411.7 KB | Display | |
Data in XML | emd_20416_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | emd_20416_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20416 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20416 | HTTPS FTP |
-Related structure data
Related structure data | 6pomMC 6pmoC 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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-Map
File | Download / File: emd_20416.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | T leader complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_20416_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : T-box-tRNAGly complex
Entire | Name: T-box-tRNAGly complex |
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Components |
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-Supramolecule #1: T-box-tRNAGly complex
Supramolecule | Name: T-box-tRNAGly complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
Molecular weight | Theoretical: 75 KDa |
-Macromolecule #1: T-box GlyQS leader (155-MER)
Macromolecule | Name: T-box GlyQS leader (155-MER) / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
Molecular weight | Theoretical: 54.730551 KDa |
Sequence | String: GUUGCAGUGA GAGAAAGAAG UACUUGCGUU ACCUCAUGAA AGCGACCUUA GGGCGGUGUA AGCUAAGGAU GAGCACGCAA CGAAAGGCA UUCUUGAGCA AUUUUAAAAA AGAGGCUGGG AUUUUGUUCU CAGCAACUAG GGUGGAACCG CGGGAGAACU C UCGUCCCU A GENBANK: GENBANK: D84432.1 |
-Macromolecule #2: tRNAGly (75-MER)
Macromolecule | Name: tRNAGly (75-MER) / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
Molecular weight | Theoretical: 24.156336 KDa |
Sequence | String: GCGGAAGUAG UUCAGUGGUA GAACACCACC UUGCCAAGGU GGGGGUCGCG GGUUCGAAUC CCGUCUUCCG CUCCA GENBANK: GENBANK: CP035163.1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.25 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV / Details: 3 uL sample blot once for 3s. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 79.0 K / Max: 79.0 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-25 / Number grids imaged: 3 / Number real images: 5600 / Average exposure time: 5.0 sec. / Average electron dose: 38.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: model map cross correlation | ||||||
Output model | PDB-6pom: |