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Yorodumi- PDB-3j8g: Electron cryo-microscopy structure of EngA bound with the 50S rib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3j8g | ||||||
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Title | Electron cryo-microscopy structure of EngA bound with the 50S ribosomal subunit | ||||||
Components |
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Keywords | RIBOSOME / 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 / negative regulation of translational initiation / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of cell growth / DNA-templated transcription termination / : / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit rRNA binding / ribosome binding / ribosomal large subunit assembly / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / transferase activity / tRNA binding / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / mRNA binding / negative regulation of DNA-templated transcription / GTP binding / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5 Å | ||||||
Authors | Zhang, X. / Yan, K. / Zhang, Y. / Li, N. / Ma, C. / Li, Z. / Zhang, Y. / Feng, B. / Liu, J. / Sun, Y. ...Zhang, X. / Yan, K. / Zhang, Y. / Li, N. / Ma, C. / Li, Z. / Zhang, Y. / Feng, B. / Liu, J. / Sun, Y. / Xu, Y. / 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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3j8g.cif.gz | 2.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3j8g.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 3j8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/3j8g ftp://data.pdbj.org/pub/pdb/validation_reports/j8/3j8g | HTTPS FTP |
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-Related structure data
Related structure data | 6149MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 2 types, 2 molecules AB
#1: RNA chain | Mass: 37848.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: GenBank: CP009578.1 |
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#2: RNA chain | Mass: 941306.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / References: GenBank: HG738867.1 |
+50S ribosomal protein ... , 29 types, 29 molecules 0KL1MNOPQRSDT2UWEY35678CFGHIJ
-Protein , 1 types, 1 molecules X
#19: Protein | Mass: 55110.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C9QPR2, UniProt: P0A6P5*PLUS |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Buffer solution | pH: 7.5 | ||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Apr 1, 2012 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Camera length: 0 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Film or detector model: FEI EAGLE (4k x 4k) |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software | Name: RELION / Category: 3D reconstruction | |||||||||||||||||||||
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Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Resolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 189614 / Details: Single particle--Applied symmetry: C1 / Symmetry type: POINT | |||||||||||||||||||||
Atomic model building |
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Atomic model building |
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Refinement step | Cycle: LAST
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