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Yorodumi- EMDB-6149: Electron cryo-microscopy structure of EngA bound with the 50S rib... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6149 | |||||||||
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Title | Electron cryo-microscopy structure of EngA bound with the 50S ribosomal subunit | |||||||||
Map data | Reconstruction of E. coli 50S subunit and EngA | |||||||||
Sample |
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Keywords | Ribosome assembly / EngA / Der / YphC / GTPase / RNA folding | |||||||||
Function / homology | Function and homology information GTPase activating protein binding / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination ...GTPase activating protein binding / guanosine tetraphosphate binding / stringent response / ribosomal large subunit binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / GTPase activity / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.0 Å | |||||||||
Authors | Zhang X / Yan K / Lei J / Gao N | |||||||||
Citation | Journal: Nucleic Acids Res / Year: 2014 Title: Structural insights into the function of a unique tandem GTPase EngA in bacterial ribosome assembly. Authors: Xiaoxiao Zhang / Kaige Yan / Yixiao Zhang / Ningning Li / Chengying Ma / Zhifei Li / Yanqing Zhang / Boya Feng / Jing Liu / Yadong Sun / Yanji Xu / Jianlin Lei / Ning Gao / Abstract: Many ribosome-interacting GTPases, with proposed functions in ribosome biogenesis, are also implicated in the cellular regulatory coupling between ribosome assembly process and various growth control ...Many ribosome-interacting GTPases, with proposed functions in ribosome biogenesis, are also implicated in the cellular regulatory coupling between ribosome assembly process and various growth control pathways. EngA is an essential GTPase in bacteria, and intriguingly, it contains two consecutive GTPase domains (GD), being one-of-a-kind among all known GTPases. EngA is required for the 50S subunit maturation. However, its molecular role remains elusive. Here, we present the structure of EngA bound to the 50S subunit. Our data show that EngA binds to the peptidyl transferase center (PTC) and induces dramatic conformational changes on the 50S subunit, which virtually returns the 50S subunit to a state similar to that of the late-stage 50S assembly intermediates. Very interestingly, our data show that the two GDs exhibit a pseudo-two-fold symmetry in the 50S-bound conformation. Our results indicate that EngA recognizes certain forms of the 50S assembly intermediates, and likely facilitates the conformational maturation of the PTC of the 23S rRNA in a direct manner. Furthermore, in a broad context, our data also suggest that EngA might be a sensor of the cellular GTP/GDP ratio, endowed with multiple conformational states, in response to fluctuations in cellular nucleotide pool, to facilitate and regulate ribosome assembly. | |||||||||
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_6149.map.gz | 115 MB | EMDB map data format | |
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Header (meta data) | emd-6149-v30.xml emd-6149.xml | 9.2 KB 9.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6149_fsc.xml | 10.9 KB | Display | FSC data file |
Images | 400_6149.gif 80_6149.gif | 41.9 KB 2.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6149 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6149 | HTTPS FTP |
-Validation report
Summary document | emd_6149_validation.pdf.gz | 422 KB | Display | EMDB validaton report |
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Full document | emd_6149_full_validation.pdf.gz | 421.5 KB | Display | |
Data in XML | emd_6149_validation.xml.gz | 11.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6149 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6149 | HTTPS FTP |
-Related structure data
Related structure data | 3j8gMC 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_6149.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of E. coli 50S subunit and EngA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1659 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 : EngA bound with E. coli 50S subunit
Entire | Name: EngA bound with E. coli 50S subunit |
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Components |
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-Supramolecule #1000: EngA bound with E. coli 50S subunit
Supramolecule | Name: EngA bound with E. coli 50S subunit / type: sample / ID: 1000 / Number unique components: 2 |
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-Supramolecule #1: 50S ribosome
Supramolecule | Name: 50S ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI Ribosome-details: ribosome-prokaryote: LSU 50S, LSU RNA 23S, LSU RNA 5S |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
-Macromolecule #1: EngA
Macromolecule | Name: EngA / type: protein_or_peptide / ID: 1 / Name.synonym: Der / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: BL21(DE3) / Recombinant plasmid: pET28a |
-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 / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Apr 1, 2012 |
Image recording | Category: CCD / Film or detector model: FEI EAGLE (4k x 4k) |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 189614 |
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FSC plot (resolution estimation) |
-Atomic model buiding 1
Initial model | PDB ID: 2wwq |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-3j8g: |