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Yorodumi- PDB-2dyj: Crystal structure of ribosome-binding factor A from Thermus therm... -
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-Basic information
Entry | Database: PDB / ID: 2dyj | ||||||
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Title | Crystal structure of ribosome-binding factor A from Thermus thermophilus HB8 | ||||||
Components | Ribosome-binding factor A | ||||||
Keywords | RIBOSOMAL PROTEIN / 16S rRNA processing / 17S RNA / KH domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Kawazoe, M. / Takemoto, C. / Nakayama-Ushikoshi, R. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Mol Cell / Year: 2007 Title: Structural aspects of RbfA action during small ribosomal subunit assembly. Authors: Partha P Datta / Daniel N Wilson / Masahito Kawazoe / Neil K Swami / Tatsuya Kaminishi / Manjuli R Sharma / Timothy M Booth / Chie Takemoto / Paola Fucini / Shigeyuki Yokoyama / Rajendra K Agrawal / Abstract: Ribosome binding factor A (RbfA) is a bacterial cold shock response protein, required for an efficient processing of the 5' end of the 16S ribosomal RNA (rRNA) during assembly of the small (30S) ...Ribosome binding factor A (RbfA) is a bacterial cold shock response protein, required for an efficient processing of the 5' end of the 16S ribosomal RNA (rRNA) during assembly of the small (30S) ribosomal subunit. Here we present a crystal structure of Thermus thermophilus (Tth) RbfA and a three-dimensional cryo-electron microscopic (EM) map of the Tth 30S*RbfA complex. RbfA binds to the 30S subunit in a position overlapping the binding sites of the A and P site tRNAs, and RbfA's functionally important C terminus extends toward the 5' end of the 16S rRNA. In the presence of RbfA, a portion of the 16S rRNA encompassing helix 44, which is known to be directly involved in mRNA decoding and tRNA binding, is displaced. These results shed light on the role played by RbfA during maturation of the 30S subunit, and also indicate how RbfA provides cells with a translational advantage under conditions of cold shock. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dyj.cif.gz | 50.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dyj.ent.gz | 35.6 KB | Display | PDB format |
PDBx/mmJSON format | 2dyj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/2dyj ftp://data.pdbj.org/pub/pdb/validation_reports/dy/2dyj | HTTPS FTP |
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-Related structure data
Related structure data | 1413C 2r1cC 2r1gC 1josS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 10875.709 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0907 / Plasmid: pET11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SJV1 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.2M Ammonium dihydrogen phosphate, 0.08M Tris-HCl pH8.5, 9.6% v/v Glycerol anhydrous, 0.02M Bis-Tris propane pH 7.0, 0.08M Magnesium formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 26, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→43 Å / Num. obs: 13813 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.73 % / Biso Wilson estimate: 16.6 Å2 / Rsym value: 0.061 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 1.84→1.91 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.22 / Num. unique all: 1383 / Rsym value: 0.312 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JOS Resolution: 1.84→42.92 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 591976.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.0221 Å2 / ksol: 0.373731 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.84→42.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.96 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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