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- PDB-1jgp: The Path of Messenger RNA Through the Ribosome. THIS FILE, 1JGP, ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jgp | ||||||
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Title | The Path of Messenger RNA Through the Ribosome. THIS FILE, 1JGP, CONTAINS THE 30S RIBOSOME SUBUNIT, THREE TRNA, AND MRNA MOLECULES. 50S RIBOSOME SUBUNIT IS IN THE FILE 1GIY | ||||||
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![]() | RIBOSOME / ribosome assembly / protein synthesis / life | ||||||
Function / homology | ![]() 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 / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yusupova, G.Z. / Yusupov, M.M. / Cate, J.H.D. / Noller, H.F. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 274.2 KB | Display | ![]() |
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PDB format | ![]() | 169.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.1 KB | Display | ![]() |
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Full document | ![]() | 530.1 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 54.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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) ![]() ![]() | ||||
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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: 11591.955 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: 36 nt long mRNA fragment. The actual sequence GGCAAGGAGGUAAAA AUGGUA AAACGUAAAUCAACU modeled as GGCAAGGAGGUAAAA UUUUUU AAACGUAAAUCAACU |
-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) ![]() ![]() |
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#6: Protein | Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 14429.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#13: Protein | Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#14: Protein | Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#15: Protein | Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#16: Protein | Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#17: Protein | Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#18: Protein | Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#19: Protein | Mass: 10808.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#20: Protein | Mass: 12324.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#21: Protein | Mass: 10244.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#22: Protein | Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#23: Protein | Mass: 11722.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#24: Protein/peptide | Mass: 3218.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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: 7→250 Å / Num. obs: 73146 / % possible obs: 89.5 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.088 |
Reflection | *PLUS Lowest resolution: 250 Å / Rmerge(I) obs: 0.088 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() 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: 7→250 Å
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Refinement | *PLUS Highest resolution: 7 Å / Lowest resolution: 250 Å / σ(F): 0 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |