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Yorodumi- PDB-4wcw: Ribosomal silencing factor during starvation or stationary phase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wcw | |||||||||
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Title | Ribosomal silencing factor during starvation or stationary phase (RsfS) from Mycobacterium tuberculosis | |||||||||
Components | Ribosomal silencing factor RsfS | |||||||||
Keywords | TRANSLATION / Tuberculosis Ribosomal Silencing dimer / Structural Genomics / TB Structural Genomics Consortium / TBSGC | |||||||||
Function / homology | Function and homology information negative regulation of ribosome biogenesis / ribosomal large subunit binding / cytosolic ribosome assembly / negative regulation of translation / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Li, X. / Sun, Q. / Jiang, C. / Yang, K. / Hung, L. / Zhang, J. / Sacchettini, J. / TB Structural Genomics Consortium (TBSGC) | |||||||||
Funding support | United States, 2items
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Citation | Journal: Structure / Year: 2015 Title: Structure of Ribosomal Silencing Factor Bound to Mycobacterium tuberculosis Ribosome. Authors: Xiaojun Li / Qingan Sun / Cai Jiang / Kailu Yang / Li-Wei Hung / Junjie Zhang / James C Sacchettini / Abstract: The ribosomal silencing factor RsfS slows cell growth by inhibiting protein synthesis during periods of diminished nutrient availability. The crystal structure of Mycobacterium tuberculosis (Mtb) ...The ribosomal silencing factor RsfS slows cell growth by inhibiting protein synthesis during periods of diminished nutrient availability. The crystal structure of Mycobacterium tuberculosis (Mtb) RsfS, together with the cryo-electron microscopy (EM) structure of the large subunit 50S of Mtb ribosome, reveals how inhibition of protein synthesis by RsfS occurs. RsfS binds to the 50S at L14, which, when occupied, blocks the association of the small subunit 30S. Although Mtb RsfS is a dimer in solution, only a single subunit binds to 50S. The overlap between the dimer interface and the L14 binding interface confirms that the RsfS dimer must first dissociate to a monomer in order to bind to L14. RsfS interacts primarily through electrostatic and hydrogen bonding to L14. The EM structure shows extended rRNA density that it is not found in the Escherichia coli ribosome, the most striking of these being the extended RNA helix of H54a. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wcw.cif.gz | 113.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wcw.ent.gz | 85.1 KB | Display | PDB format |
PDBx/mmJSON format | 4wcw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wcw_validation.pdf.gz | 465.6 KB | Display | wwPDB validaton report |
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Full document | 4wcw_full_validation.pdf.gz | 471.4 KB | Display | |
Data in XML | 4wcw_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 4wcw_validation.cif.gz | 33.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/4wcw ftp://data.pdbj.org/pub/pdb/validation_reports/wc/4wcw | HTTPS FTP |
-Related structure data
Related structure data | 6177C 6178C 2o5aS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | Dimer confirmed by gel filtration |
-Components
#1: Protein | Mass: 15277.115 Da / Num. of mol.: 4 / Mutation: Y102A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: rsfS, Rv2420c, P425_02518, RVBD_2420c / Production host: Mycobacterium smegmatis (bacteria) / References: UniProt: O86327 #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.13 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M Sodium Cacodylate pH6.5, 0.2 M Magnesium Acetate, 30% MPD |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46.06 Å / Num. obs: 49832 / % possible obs: 93.3 % / Redundancy: 1.7 % / Net I/σ(I): 6.3 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O5A Resolution: 2.1→46.06 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 25.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.06 Å
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Refine LS restraints |
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LS refinement shell |
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