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Yorodumi- PDB-1zax: Ribosomal Protein L10-L12(NTD) Complex, Space Group P212121, Form B -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zax | ||||||
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Title | Ribosomal Protein L10-L12(NTD) Complex, Space Group P212121, Form B | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / ribosome structure and function / L10-L12 complex structure / L10E structure / L7/12 ribosomal stalk / thiostrepton loop of 23S rRNA / translation factor recruitment / GTPase stimulation / mechanism of translation / rapid kinetics | ||||||
Function / homology | Function and homology information large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / structural constituent of ribosome / translation / mRNA binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Diaconu, M. / Kothe, U. / Schluenzen, F. / Fischer, N. / Harms, J.M. / Tonevitski, A.G. / Stark, H. / Rodnina, M.V. / Wahl, M.C. | ||||||
Citation | Journal: Cell / Year: 2005 Title: Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation. Authors: Mihaela Diaconu / Ute Kothe / Frank Schlünzen / Niels Fischer / Jörg M Harms / Alexander G Tonevitsky / Holger Stark / Marina V Rodnina / Markus C Wahl / Abstract: The L7/12 stalk of the large subunit of bacterial ribosomes encompasses protein L10 and multiple copies of L7/12. We present crystal structures of Thermotoga maritima L10 in complex with three L7/12 ...The L7/12 stalk of the large subunit of bacterial ribosomes encompasses protein L10 and multiple copies of L7/12. We present crystal structures of Thermotoga maritima L10 in complex with three L7/12 N-terminal-domain dimers, refine the structure of an archaeal L10E N-terminal domain on the 50S subunit, and identify these elements in cryo-electron-microscopic reconstructions of Escherichia coli ribosomes. The mobile C-terminal helix alpha8 of L10 carries three L7/12 dimers in T. maritima and two in E. coli, in concordance with the different length of helix alpha8 of L10 in these organisms. The stalk is organized into three elements (stalk base, L10 helix alpha8-L7/12 N-terminal-domain complex, and L7/12 C-terminal domains) linked by flexible connections. Highly mobile L7/12 C-terminal domains promote recruitment of translation factors to the ribosome and stimulate GTP hydrolysis by the ribosome bound factors through stabilization of their active GTPase conformation. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zax.cif.gz | 86.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zax.ent.gz | 66.8 KB | Display | PDB format |
PDBx/mmJSON format | 1zax.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zax_validation.pdf.gz | 471.9 KB | Display | wwPDB validaton report |
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Full document | 1zax_full_validation.pdf.gz | 480.8 KB | Display | |
Data in XML | 1zax_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 1zax_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/1zax ftp://data.pdbj.org/pub/pdb/validation_reports/za/1zax | 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
#1: Protein | Mass: 20436.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: rplJ / Production host: Escherichia coli (E. coli) / References: UniProt: P29394 | ||
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#2: Protein/peptide | Mass: 3409.979 Da / Num. of mol.: 6 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: rplL / Production host: Escherichia coli (E. coli) / References: UniProt: P29396 #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: imidazole, MgCl2, MPD, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 19, 2004 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 24744 / Num. obs: 24199 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.1→2.2 Å / % possible all: 96.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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