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Yorodumi- PDB-4v9h: Crystal structure of the ribosome bound to elongation factor G in... -
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-Basic information
Entry | Database: PDB / ID: 4v9h | |||||||||
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Title | Crystal structure of the ribosome bound to elongation factor G in the guanosine triphosphatase state | |||||||||
Components |
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Keywords | RIBOSOME / Bacterial Proteins / Catalysis / Models / Molecular / Peptide Elongation Factor G / Protein Biosynthesis / Protein Conformation / Protein Structure / Tertiary / RNA / Bacterial / Messenger / Transfer / Ribosomes / Thermus thermophilus / Hybrid state / Guanosine triphosphate / Guanosine triphosphatase | |||||||||
Function / homology | Function and homology information ribosome disassembly / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / translation elongation factor activity / large ribosomal subunit / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding ...ribosome disassembly / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / translation elongation factor activity / large ribosomal subunit / regulation of translation / 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 / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Thermus thermophilus (bacteria) Escherichia coli (E. coli) Synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.857 Å | |||||||||
Authors | Tourigny, D.S. / Fernandez, I.S. / Kelley, A.C. / Ramakrishnan, V. | |||||||||
Citation | Journal: Science / Year: 2013 Title: Elongation factor G bound to the ribosome in an intermediate state of translocation. Authors: Tourigny, D.S. / Fernandez, I.S. / 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 | 4v9h.cif.gz | 3.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v9h.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v9h_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 4v9h_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 4v9h_validation.xml.gz | 373.4 KB | Display | |
Data in CIF | 4v9h_validation.cif.gz | 541.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/4v9h ftp://data.pdbj.org/pub/pdb/validation_reports/v9/4v9h | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-RNA chain , 5 types, 5 molecules AAAVAXBABB
#1: RNA chain | Mass: 492082.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 55771382 |
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#2: RNA chain | Mass: 24485.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 169887498 |
#3: RNA chain | Mass: 8156.980 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) |
#25: RNA chain | Mass: 947935.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 55771382 |
#26: RNA chain | Mass: 39540.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 55771382 |
-30S ribosomal protein ... , 20 types, 20 molecules AJAKALAMANAOAPAQARASATABACADAEAFAGAHAIAU
#4: Protein | Mass: 11299.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN7 |
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#5: Protein | Mass: 12606.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80376 |
#6: Protein | Mass: 13804.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHN3 |
#7: Protein | Mass: 14078.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80377 |
#8: Protein | Mass: 7027.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS |
#9: Protein | Mass: 10447.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJ76 |
#10: Protein | Mass: 9924.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJH3 |
#11: Protein | Mass: 11722.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS |
#12: Protein | Mass: 8155.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLQ0 |
#13: Protein | Mass: 8949.435 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHP2 |
#14: Protein | Mass: 10921.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80380 |
#15: Protein | Mass: 26987.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80371 |
#16: Protein | Mass: 22862.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80372 |
#17: Protein | Mass: 24242.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80373 |
#18: Protein | Mass: 16331.079 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ5 |
#19: Protein | Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SLP8 |
#20: Protein | Mass: 17919.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P17291 |
#21: Protein | Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS |
#22: Protein | Mass: 14298.466 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P80374 |
#24: Protein/peptide | Mass: 2960.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SIH3 |
-Protein , 1 types, 1 molecules AY
#23: Protein | Mass: 75741.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: EFG / Plasmid: pLysS / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SHN5 |
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+50S ribosomal protein ... , 32 types, 32 molecules BNBOBPBQBRBSBTBUBVBWBXBYBZB0B1B2BDB3B4B5B6B7B8B9BCBEBFBGBHBKBJBL
-Non-polymers , 3 types, 143 molecules
#59: Chemical | ChemComp-MG / #60: Chemical | ChemComp-GCP / | #61: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.45 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 100mM MES pH 6.3, 75mM KCl, 6.0% PEG 20K, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction |
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Diffraction source |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.857→39.6 Å / Num. all: 635092 / Num. obs: 635092 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.22 / Net I/σ(I): 7.56 | |||||||||||||||
Reflection shell | Resolution: 2.857→3 Å / Mean I/σ(I) obs: 1.02 / Rsym value: 1.38 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.857→39.6 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 277.27 Å2 / Biso mean: 45.9069 Å2 / Biso min: 2 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.857→39.6 Å
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LS refinement shell | Resolution: 2.857→2.931 Å
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