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- PDB-5gio: Crystal structure of box C/D RNP with 12 nt guide regions and 13 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gio | ||||||
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Title | Crystal structure of box C/D RNP with 12 nt guide regions and 13 nt substrates | ||||||
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![]() | TRANSFERASE/RNA / 2'-O-methylation / guide RNA / RNP / TRANSFERASE-RNA complex | ||||||
Function / homology | ![]() box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / box C/D methylation guide snoRNP complex / ribonuclease P activity / tRNA 5'-leader removal / rRNA methylation / histone H2A Q104 methyltransferase activity / tRNA processing / snoRNA binding / Transferases; Transferring one-carbon groups; Methyltransferases ...box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / box C/D methylation guide snoRNP complex / ribonuclease P activity / tRNA 5'-leader removal / rRNA methylation / histone H2A Q104 methyltransferase activity / tRNA processing / snoRNA binding / Transferases; Transferring one-carbon groups; Methyltransferases / ribosome biogenesis / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, Z. / Lin, J. / Ye, K. | ||||||
![]() | ![]() Title: Box C/D guide RNAs recognize a maximum of 10 nt of substrates Authors: Yang, Z. / Lin, J. / Ye, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 505.4 KB | Display | ![]() |
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PDB format | ![]() | 406.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 78.7 KB | Display | |
Data in CIF | ![]() | 108.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ginC ![]() 5gipC ![]() 3plaS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 3 types, 9 molecules ABKCDLEFM
#1: Protein | Mass: 44168.531 Da / Num. of mol.: 3 / Fragment: UNP residues 3-379 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 14075.301 Da / Num. of mol.: 3 / Fragment: UNP residues 3-127 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein | Mass: 26439.375 Da / Num. of mol.: 3 / Fragment: UNP residues 3-232 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A0E3JUC9, UniProt: P58032*PLUS, Transferases; Transferring one-carbon groups; Methyltransferases |
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-RNA chain , 2 types, 6 molecules GHNIJO
#4: RNA chain | Mass: 12852.657 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #5: RNA chain | Mass: 4181.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Non-polymers , 1 types, 3 molecules 
#6: Chemical |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2.0M ammonium sulfate, 2%(v/v) PEG400, 10mM magnesium chloride, 0.1M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→20 Å / Num. obs: 49349 / % possible obs: 99.7 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.165 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 3.6→3.66 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3PLA Resolution: 3.604→19.957 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 30.15
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.604→19.957 Å
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Refine LS restraints |
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LS refinement shell |
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