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- PDB-4jkd: Open and closed forms of I1790Y human PRP8 RNase H-like domain wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jkd | ||||||
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Title | Open and closed forms of I1790Y human PRP8 RNase H-like domain with bound Mg ion | ||||||
![]() | Pre-mRNA-processing-splicing factor 8 | ||||||
![]() | RNA BINDING PROTEIN / metalloprotein / conformational change | ||||||
Function / homology | ![]() U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / U2-type catalytic step 2 spliceosome / K63-linked polyubiquitin modification-dependent protein binding / mRNA Splicing - Minor Pathway / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding ...U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / U2-type catalytic step 2 spliceosome / K63-linked polyubiquitin modification-dependent protein binding / mRNA Splicing - Minor Pathway / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / RNA splicing / mRNA Splicing - Major Pathway / mRNA processing / mRNA splicing, via spliceosome / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / nuclear speck / RNA binding / nucleoplasm / membrane / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schellenberg, M.J. / Wu, T. / Ritchie, D.B. / Atta, K.A. / MacMillan, A.M. | ||||||
![]() | ![]() Title: A conformational switch in PRP8 mediates metal ion coordination that promotes pre-mRNA exon ligation. Authors: Schellenberg, M.J. / Wu, T. / Ritchie, D.B. / Fica, S. / Staley, J.P. / Atta, K.A. / Lapointe, P. / Macmillan, A.M. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 225.6 KB | Display | ![]() |
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PDB format | ![]() | 180.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.4 KB | Display | ![]() |
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Full document | ![]() | 447.9 KB | Display | |
Data in XML | ![]() | 26 KB | Display | |
Data in CIF | ![]() | 40.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jk7C ![]() 4jk8C ![]() 4jk9C ![]() 4jkaC ![]() 4jkbC ![]() 4jkcC ![]() 4jkeC ![]() 4jkfC ![]() 4jkgC ![]() 4jkhC ![]() 3enbS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 25588.803 Da / Num. of mol.: 2 / Fragment: PRP8 RNase H-like domain, UNP residues 1769-1990' / Mutation: I1790Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: 15% PEG 4000, 300mM MgCl2, 100mM Tris, pH 7.5, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 22, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1158 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→50 Å / Num. all: 79587 / Num. obs: 79587 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.05 / Χ2: 1.024 / Net I/σ(I): 15.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3ENB Resolution: 1.55→40.28 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.1886 / WRfactor Rwork: 0.1481 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9071 / SU B: 2.522 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0795 / SU Rfree: 0.0719 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.15 Å2 / Biso mean: 21.3857 Å2 / Biso min: 6.71 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→40.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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