+Open data
-Basic information
Entry | Database: PDB / ID: 1j5e | |||||||||
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Title | Structure of the Thermus thermophilus 30S Ribosomal Subunit | |||||||||
Components |
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Keywords | RIBOSOME / 30S RIBOSOMAL SUBUNIT | |||||||||
Function / homology | Function and homology information ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermus thermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.05 Å | |||||||||
Authors | Wimberly, B.T. / Brodersen, D.E. / Clemons Jr., W.M. / Morgan-Warren, R. / Carter, A.P. / Vonrhein, C. / Hartsch, T. / Ramakrishnan, V. | |||||||||
Citation | Journal: Nature / Year: 2000 Title: Structure of the 30S ribosomal subunit. Authors: B T Wimberly / D E Brodersen / W M Clemons / R J Morgan-Warren / A P Carter / C Vonrhein / T Hartsch / V Ramakrishnan / Abstract: Genetic information encoded in messenger RNA is translated into protein by the ribosome, which is a large nucleoprotein complex comprising two subunits, denoted 30S and 50S in bacteria. Here we ...Genetic information encoded in messenger RNA is translated into protein by the ribosome, which is a large nucleoprotein complex comprising two subunits, denoted 30S and 50S in bacteria. Here we report the crystal structure of the 30S subunit from Thermus thermophilus, refined to 3 A resolution. The final atomic model rationalizes over four decades of biochemical data on the ribosome, and provides a wealth of information about RNA and protein structure, protein-RNA interactions and ribosome assembly. It is also a structural basis for analysis of the functions of the 30S subunit, such as decoding, and for understanding the action of antibiotics. The structure will facilitate the interpretation in molecular terms of lower resolution structural data on several functional states of the ribosome from electron microscopy and crystallography. #1: Journal: Nature / Year: 2000 Title: Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics Authors: Carter, A.P. / Clemons Jr., W.M. / Brodersen, D.E. / Wimberly, B.T. / Morgan-Warren, R. / Ramakrishnan, V. #2: Journal: Nature / Year: 1999 Title: Structure of a Bacterial 30S Ribosomal Subunit at 5.5 A Resolution Authors: Clemons Jr., W.M. / May, J.L.C. / Wimberly, B.T. / McCutcheon, J.P. / Capel, M.S. / Ramakrishnan, V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j5e.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1j5e.ent.gz | 932.4 KB | Display | PDB format |
PDBx/mmJSON format | 1j5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/1j5e ftp://data.pdbj.org/pub/pdb/validation_reports/j5/1j5e | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-RNA chain , 1 types, 1 molecules A
#1: RNA chain | Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 155076 |
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-30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTV
#2: Protein | Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 13446664, UniProt: P80371*PLUS |
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#3: Protein | Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 13446666, UniProt: P80372*PLUS |
#4: Protein | Mass: 24242.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80373 |
#5: Protein | Mass: 17452.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P27152, UniProt: Q5SHQ5*PLUS |
#6: Protein | Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P23370, UniProt: Q5SLP8*PLUS |
#7: Protein | Mass: 17919.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P17291 |
#8: Protein | Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P24319, UniProt: P0DOY9*PLUS |
#9: Protein | Mass: 14429.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 13446668, UniProt: P80374*PLUS |
#10: Protein | Mass: 11823.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80375, UniProt: Q5SHN7*PLUS |
#11: Protein | Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 4519421, UniProt: P80376*PLUS |
#12: Protein | Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P17293, UniProt: Q5SHN3*PLUS |
#13: Protein | Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 4519420, UniProt: P80377*PLUS |
#14: Protein | Mass: 7027.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P24320, UniProt: P0DOY6*PLUS |
#15: Protein | Mass: 10447.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80378, UniProt: Q5SJ76*PLUS |
#16: Protein | Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80379, UniProt: Q5SJH3*PLUS |
#17: Protein | Mass: 12193.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P24321, UniProt: P0DOY7*PLUS |
#18: Protein | Mass: 10244.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: EMBL: 6739549, UniProt: Q5SLQ0*PLUS |
#19: Protein | Mass: 10474.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80381, UniProt: Q5SHP2*PLUS |
#20: Protein | Mass: 11722.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: EMBL: 11125386, UniProt: P80380*PLUS |
#21: Protein/peptide | Mass: 3218.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P32193, UniProt: Q5SIH3*PLUS |
-Non-polymers , 2 types, 190 molecules
#22: Chemical | ChemComp-UNX / #23: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 6 |
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-Sample preparation
Crystal | Density Matthews: 4.53 Å3/Da / Density meas: 4.167 Mg/m3 / Density % sol: 70.51 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MPD, NH4Cl, KCl, CaCl2, magnesium acetate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Details: Trakhanov, S.D., (1987) FEBS Lett., 220, 319. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.05→59.761 Å / Num. all: 254610 / Num. obs: 254610 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 68.711 Å2 / Rsym value: 0.132 / Net I/σ(I): 8.1 | |||||||||||||||
Reflection shell | Resolution: 3.05→3.16 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 24241 / Rsym value: 0.612 / % possible all: 90.3 | |||||||||||||||
Reflection | *PLUS Highest resolution: 3.05 Å / Num. measured all: 840101 / Rmerge(I) obs: 0.108 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 81.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 3.05→59.761 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 Stereochemistry target values: proteins: Engh & Huber, RNA: Parkinson at al. Details: ML TARGET WITH PHASE RESTRAINTS USED IN THE FIRST COUPLE OF CYCLES, THEN ML REFINEMENT AGAINST AMPLITUDES ONLY. METAL IONS (RESIDUES UNX) WERE REFINED AS COBALT CATIONS BUT SOME OF THEM ...Details: ML TARGET WITH PHASE RESTRAINTS USED IN THE FIRST COUPLE OF CYCLES, THEN ML REFINEMENT AGAINST AMPLITUDES ONLY. METAL IONS (RESIDUES UNX) WERE REFINED AS COBALT CATIONS BUT SOME OF THEM MIGHT BE MAGNESIUM CATIONS
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Solvent computation | Solvent model: CNS MASK MODE / Bsol: 30.089 Å2 / ksol: 0.27759 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.51 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.05→59.761 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.05→3.11 Å / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Lowest resolution: 99 Å / % reflection Rfree: 5 % / Rfactor obs: 0.208 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.362 |