+Open data
-Basic information
Entry | Database: PDB / ID: 4v7p | |||||||||
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Title | Recognition of the amber stop codon by release factor RF1. | |||||||||
Components |
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Keywords | RIBOSOME / 70S / termination / release factor / RF1 / amber / stop codon / UAG | |||||||||
Function / homology | Function and homology information translation release factor activity, codon specific / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...translation release factor activity, codon specific / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermus thermophilus (bacteria) Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.62 Å | |||||||||
Authors | Korostelev, A. / Zhu, J. / Asahara, H. / Noller, H.F. | |||||||||
Citation | Journal: Embo J. / Year: 2010 Title: Recognition of the amber UAG stop codon by release factor RF1. Authors: Korostelev, A. / Zhu, J. / Asahara, 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 | 4v7p.cif.gz | 6.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v7p.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/4v7p ftp://data.pdbj.org/pub/pdb/validation_reports/v7/4v7p | HTTPS FTP |
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-Related structure data
Related structure data | 3f1e 3f1f S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-RNA chain , 4 types, 8 molecules AADAAWDWBACABBCB
#1: RNA chain | Mass: 488431.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: GenBank: AE017221.1 #23: RNA chain | Mass: 24802.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: BL21(DE3) / References: GenBank: CP001509.3 #25: RNA chain | Mass: 936302.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: GenBank: AE017221.1 #26: RNA chain | Mass: 38553.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: GenBank: AE017221.1 |
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-30S ribosomal protein ... , 20 types, 40 molecules ABDBACDCADDDAEDEAFDFAGDGAHDHAIDIAJDJAKDKALDLAMDMANDNAODOAPDP...
#2: Protein | Mass: 26987.271 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62662 #3: Protein | Mass: 22862.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62663 #4: Protein | Mass: 24242.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62664 #5: Protein | Mass: 16460.193 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62665 #6: Protein | Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62666 #7: Protein | Mass: 17919.775 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62667 #8: Protein | Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62668 #9: Protein | Mass: 14298.466 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62669 #10: Protein | Mass: 11299.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62653 #11: Protein | Mass: 12606.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62654 #12: Protein | Mass: 13804.311 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P61941 #13: Protein | Mass: 13308.508 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62655 #14: Protein | Mass: 7027.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62656 #15: Protein | Mass: 10447.213 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62657 #16: Protein | Mass: 9924.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62238 #17: Protein | Mass: 11721.919 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62658 #18: Protein | Mass: 8155.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62659 #19: Protein | Mass: 8949.435 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62660 #20: Protein | Mass: 10907.060 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62661 #21: Protein/peptide | Mass: 2960.475 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: P62613 |
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-Protein , 1 types, 2 molecules AVDV
#22: Protein | Mass: 40153.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 / References: UniProt: Q72HB8 |
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-Messenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)- ... , 2 types, 2 molecules AXDX
#24: RNA chain | Mass: 2245.403 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 |
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#56: RNA chain | Mass: 2903.815 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB27 |
+50S ribosomal protein ... , 29 types, 58 molecules BCCCBDCDBECEBFCFBGCGBHCHBICIBJCJBKCKBLCLBMCMBNCNBOCOBPCPBQCQ...
-Non-polymers , 2 types, 414 molecules
#57: Chemical | ChemComp-MG / #58: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 8 |
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-Sample preparation
Crystal | Density Matthews: 3.339 Å3/Da / Density % sol: 61.75 % |
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Crystal grow | Temperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 7 Details: crystals were grown by the sitting-drop vapor diffusion method dispensed robotically using 1-2 uL ribosome complexes mixed with 1-2 uL reservoir solution (100 mM Tris-OAc, pH 7.0, 200 mM ...Details: crystals were grown by the sitting-drop vapor diffusion method dispensed robotically using 1-2 uL ribosome complexes mixed with 1-2 uL reservoir solution (100 mM Tris-OAc, pH 7.0, 200 mM KSCN, 3.4-4.8% PEG20,000, 2.5-11.5% PEG200) at 22.5 C, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Date: Aug 5, 2009 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.514→89 Å / Num. all: 724157 / Num. obs: 723953 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 3F1E and 3F1F Resolution: 3.62→49.953 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.59 / σ(F): 1.99 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.406 Å2 / ksol: 0.2 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 491.94 Å2 / Biso min: 75.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.62→49.953 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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