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Yorodumi- PDB-1jgq: The Path of Messenger RNA Through the Ribosome. THIS FILE, 1JGQ, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jgq | ||||||
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Title | The Path of Messenger RNA Through the Ribosome. THIS FILE, 1JGQ, CONTAINS THE 30S RIBOSOME SUBUNIT, THREE TRNA, AND MRNA MOLECULES. 50S RIBOSOME SUBUNIT IS IN THE FILE 1GIY | ||||||
Components |
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Keywords | RIBOSOME / ribosome assembly / protein synthesis / life | ||||||
Function / homology | Function and homology information endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / 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 ...endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / 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 / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 5 Å | ||||||
Authors | Yusupova, G.Z. / Yusupov, M.M. / Cate, J.H.D. / Noller, H.F. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2001 Title: The path of messenger RNA through the ribosome. Authors: Yusupova, G.Z. / Yusupov, M.M. / Cate, J.H. / Noller, H.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jgq.cif.gz | 274 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jgq.ent.gz | 169.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jgq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jgq_validation.pdf.gz | 474.6 KB | Display | wwPDB validaton report |
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Full document | 1jgq_full_validation.pdf.gz | 530.3 KB | Display | |
Data in XML | 1jgq_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 1jgq_validation.cif.gz | 54.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/1jgq ftp://data.pdbj.org/pub/pdb/validation_reports/jg/1jgq | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-RNA chain , 4 types, 5 molecules ABCD1
#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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#2: RNA chain | Mass: 24890.121 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: sequence naturally occurs in Saccharomyces cerevisiae References: GenBank: 176479 #3: RNA chain | | Mass: 23728.123 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: sequence naturally occurs in Saccharomyces cerevisiae #4: RNA chain | | Mass: 11568.915 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: 36 nt long mRNA fragment. The actual sequence GGCAAGGAGGUAAAA AUG UUUAAACGUAAAUCUACU modeled as GGCAAGGAGGUAAAA UUU UUUAAACGUAAAUCUACU |
-30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules EFGHIJKLMNOPQRSTUVWX
#5: Protein | Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80371 |
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#6: Protein | Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80372*PLUS |
#7: Protein | Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80373 |
#8: Protein | Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHQ5 |
#9: Protein | Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SLP8 |
#10: Protein | Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P17291 |
#11: Protein | Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS |
#12: Protein | Mass: 14429.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80374 |
#13: Protein | Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHN7 |
#14: Protein | Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80376 |
#15: Protein | Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHN3 |
#16: Protein | Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80377 |
#17: Protein | Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS |
#18: Protein | Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SJ76 |
#19: Protein | Mass: 10808.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 12056104, UniProt: Q5SJH3*PLUS |
#20: Protein | Mass: 12324.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P0DOY7*PLUS |
#21: Protein | Mass: 10244.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 6739549, UniProt: Q5SLQ0*PLUS |
#22: Protein | Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80381, UniProt: Q5SHP2*PLUS |
#23: Protein | Mass: 11722.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 11125386, UniProt: P80380*PLUS |
#24: 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 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal grow | Method: vapor diffusion / pH: 7.4 Details: 20 mM MgCl2, 100 mM KCl, 20 mM tris HCl, pH 7.4, VAPOR DIFFUSION | ||||||||||||||||||||||||||||||||||||||||||
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Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion, hanging, sitting drop / Details: Cate, J.H., (1999) Science, 285, 2095. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 5→250 Å / Num. obs: 209044 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rsym value: 0.094 |
Reflection | *PLUS Lowest resolution: 250 Å / Rmerge(I) obs: 0.094 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 5→250 Å / σ(I): 0 Details: THE MODEL WAS BUILT BY MANUAL FITTING OF INDIVIDUAL MOLECULES INTO THE EXPERIMENTAL ELECTRON DENSITY USING THE GRAPHIC PROGRAM O.
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Refinement step | Cycle: LAST / Resolution: 5→250 Å
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Refinement | *PLUS σ(F): 0 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |