+Open data
-Basic information
Entry | Database: PDB / ID: 5ady | ||||||
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Title | Cryo-EM structures of the 50S ribosome subunit bound with HflX | ||||||
Components |
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Keywords | RIBOSOME / RIBOSOME RESCUE | ||||||
Function / homology | Function and homology information ribosome disassembly / 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 ...ribosome disassembly / 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 / rescue of stalled ribosome / ribosome assembly / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / response to radiation / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / response to heat / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / negative regulation of DNA-templated transcription / mRNA binding / GTP binding / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI K-12 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | ||||||
Authors | Zhang, Y. / Mandava, C.S. / Cao, W. / Li, X. / Zhang, D. / Li, N. / Zhang, Y. / Zhang, X. / Qin, Y. / Mi, K. ...Zhang, Y. / Mandava, C.S. / Cao, W. / Li, X. / Zhang, D. / Li, N. / Zhang, Y. / Zhang, X. / Qin, Y. / Mi, K. / Lei, J. / Sanyal, S. / Gao, N. | ||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2015 Title: HflX is a ribosome-splitting factor rescuing stalled ribosomes under stress conditions. Authors: Yanqing Zhang / Chandra Sekhar Mandava / Wei Cao / Xiaojing Li / Dejiu Zhang / Ningning Li / Yixiao Zhang / Xiaoxiao Zhang / Yan Qin / Kaixia Mi / Jianlin Lei / Suparna Sanyal / Ning Gao / Abstract: Adverse cellular conditions often lead to nonproductive translational stalling and arrest of ribosomes on mRNAs. Here, we used fast kinetics and cryo-EM to characterize Escherichia coli HflX, a ...Adverse cellular conditions often lead to nonproductive translational stalling and arrest of ribosomes on mRNAs. Here, we used fast kinetics and cryo-EM to characterize Escherichia coli HflX, a GTPase with unknown function. Our data reveal that HflX is a heat shock-induced ribosome-splitting factor capable of dissociating vacant as well as mRNA-associated ribosomes with deacylated tRNA in the peptidyl site. Structural data demonstrate that the N-terminal effector domain of HflX binds to the peptidyl transferase center in a strikingly similar manner as that of the class I release factors and induces dramatic conformational changes in central intersubunit bridges, thus promoting subunit dissociation. Accordingly, loss of HflX results in an increase in stalled ribosomes upon heat shock. These results suggest a primary role of HflX in rescuing translationally arrested ribosomes under stress conditions. | ||||||
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 | 5ady.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5ady.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 5ady.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ady_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5ady_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 5ady_validation.xml.gz | 270.2 KB | Display | |
Data in CIF | 5ady_validation.cif.gz | 420 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/5ady ftp://data.pdbj.org/pub/pdb/validation_reports/ad/5ady | HTTPS FTP |
-Related structure data
Related structure data | 3133MC 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
+50S RIBOSOMAL PROTEIN ... , 31 types, 31 molecules 0123457CDEFGHIJKLMNOPQRSTUVWXYZ
-Protein , 1 types, 1 molecules 6
#7: Protein | Mass: 48392.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: A GMPPNP AND A MAGNESIUM ION ARE INCLUDED IN THIS CHAIN. Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P25519 |
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-RNA chain , 2 types, 2 molecules AB
#9: RNA chain | Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: GenBank: 507148446 |
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#10: RNA chain | Mass: 941306.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI K-12 (bacteria) / References: GenBank: 507148266 |
-Non-polymers , 2 types, 2 molecules
#35: Chemical | ChemComp-GNP / |
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#36: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 50S-HFLX COMPLEX / Type: RIBOSOME |
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Buffer solution | Name: 20MM TRIS-HCL, 100MM NH4CL, 10MM MGCL2 / pH: 7.5 / Details: 20MM TRIS-HCL, 100MM NH4CL, 10MM MGCL2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: CARBON |
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: Jan 7, 2012 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k) |
-Processing
EM software |
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Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: SINGLE PARTICLE RECONSTRUCTION / Resolution: 4.5 Å / Num. of particles: 384206 / Nominal pixel size: 1.1659 Å / Actual pixel size: 1.1659 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD -3133. (DEPOSITION ID: 13705). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Details: METHOD--MDFF REFINEMENT PROTOCOL--FLEXIBLE | ||||||||||||
Atomic model building | PDB-ID: 3FIK 3fik Accession code: 3FIK / Source name: PDB / Type: experimental model | ||||||||||||
Refinement | Highest resolution: 4.5 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 4.5 Å
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