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Yorodumi- PDB-4v5f: The structure of the ribosome with elongation factor G trapped in... -
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-Basic information
Entry | Database: PDB / ID: 4v5f | |||||||||
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Title | The structure of the ribosome with elongation factor G trapped in the post-translocational state | |||||||||
Components |
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Keywords | RIBOSOME / ZINC-FINGER / RNA-BINDING / TRANSLATION / RRNA-BINDING / PROTEIN BIOSYNTHESIS / ELONGATION FACTOR / RIBOSOMAL PROTEIN / TRNA-BINDING / TRANSLOCATION / METAL-BINDING / NUCLEOTIDE-BINDING / ELONGATION FACTOR G / RIBONUCLEOPROTEIN / PROTEIN SYNTHESIS | |||||||||
Function / homology | Function and homology information translation elongation factor activity / large ribosomal subunit rRNA binding / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome ...translation elongation factor activity / large ribosomal subunit rRNA binding / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / GTPase activity / GTP binding / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | THERMUS THERMOPHILUS (bacteria) ESCHERICHIA COLI (E. coli) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å | |||||||||
Authors | Gao, Y.-G. / Selmer, M. / Dunham, C.M. / Weixlbaumer, A. / Kelley, A.C. / Ramakrishnan, V. | |||||||||
Citation | Journal: Science / Year: 2009 Title: The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Authors: Gao, Y.G. / Selmer, M. / Dunham, C.M. / Weixlbaumer, A. / Kelley, A.C. / Ramakrishnan, V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v5f.cif.gz | 7.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v5f.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/4v5f ftp://data.pdbj.org/pub/pdb/validation_reports/v5/4v5f | HTTPS FTP |
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-Related structure data
Related structure data | 2j00 2j01 2j02 2j03 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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-Components
-RNA chain , 5 types, 12 molecules AACAAVAWCVCWAXCXBADABBDB
#1: RNA chain | Mass: 493958.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: CHAIN A (16S RNA) HAS E.COLI NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E.COLI STRUCTURE IN 2AVY. Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: GenBank: 55979969 #22: RNA chain | Mass: 24816.811 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K12 #23: RNA chain | Mass: 8156.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #35: RNA chain | Mass: 947935.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: CHAIN A (23S RNA) HAS E.COLI RESIDUE NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E. COLI STRUCTURE IN 2AW4 Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: GenBank: 55979969 #36: RNA chain | Mass: 39540.617 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: GenBank: 55979969 |
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-30S RIBOSOMAL PROTEIN ... , 20 types, 40 molecules ABCBACCCADCDAECEAFCFAGCGAHCHAICIAJCJAKCKALCLAMCMANCNAOCOAPCP...
#2: Protein | Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P80371 #3: Protein | Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P80372 #4: Protein | Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P80373 #5: Protein | Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHQ5 #6: Protein | Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SLP8 #7: Protein | Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P17291 #8: Protein | Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS #9: Protein | Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P80374 #10: Protein | Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHN7 #11: Protein | Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P80376 #12: Protein | Mass: 14637.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHN3 #13: Protein | Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P80377 #14: Protein | Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS #15: Protein | Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SJ76 #16: Protein | Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SJH3 #17: Protein | Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS #18: Protein | Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SLQ0 #19: Protein | Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHP2 #20: Protein | Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P80380 #21: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SIH3 |
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-Protein , 1 types, 2 molecules AYCY
#24: Protein | Mass: 76977.102 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHN5 |
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+50S RIBOSOMAL PROTEIN ... , 32 types, 70 molecules B0D0B1D1B2D2B3D3B4D4B5D5B6D6B7D7B8D8B9D9BCDCBDDDBEDEBFDFBGDG...
-Non-polymers , 4 types, 14 molecules
#59: Chemical | ChemComp-ZN / #60: Chemical | #61: Chemical | #62: Chemical | |
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-Details
Nonpolymer details | THE PLACEMENT OF FUSIDIC ACID IN DENSITY IS AMBIGUOUS SO DETAILS OF SPECIFIC INTERACTIONS WITH THE ...THE PLACEMENT OF FUSIDIC ACID IN DENSITY IS AMBIGUOUS SO DETAILS OF SPECIFIC INTERACTIO |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.02 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 100 MM MES PH 6.5, 12%PEG 20K, 50 MM KCL, 10 MM NH4CL, 3UM DEOXY-BIG-CHAP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Details: DYNAMICALLY BENDABLE MIRROR |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→50 Å / Num. obs: 690340 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.37 / Net I/σ(I): 6.64 |
Reflection shell | Resolution: 3.6→3.7 Å / Redundancy: 6.91 % / Rmerge(I) obs: 1.15 / Mean I/σ(I) obs: 1.54 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2J00, 2J01, 2J02, 2J03. Resolution: 3.6→50 Å / Rfactor Rfree error: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.19 Å2 / ksol: 0.25 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 86.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.6→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.6→3.83 Å / Rfactor Rfree error: 0.004 / Total num. of bins used: 6
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