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Yorodumi- PDB-4jkg: Open and closed forms of mixed T1789P+R1865A and R1865A human PRP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jkg | ||||||
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Title | Open and closed forms of mixed T1789P+R1865A and R1865A human PRP8 RNase H-like domain with bound Mg ion | ||||||
Components | (Pre-mRNA-processing-splicing factor 8) x 2 | ||||||
Keywords | RNA BINDING PROTEIN / metalloprotein / conformational change | ||||||
Function / homology | Function and homology information RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / 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 ...RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / 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 / mRNA Splicing - Major Pathway / RNA splicing / mRNA splicing, via spliceosome / mRNA processing / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / nuclear speck / RNA binding / nucleoplasm / membrane / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Schellenberg, M.J. / Wu, T. / Ritchie, D.B. / Atta, K.A. / MacMillan, A.M. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2013 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jkg.cif.gz | 113.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jkg.ent.gz | 85.2 KB | Display | PDB format |
PDBx/mmJSON format | 4jkg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jkg_validation.pdf.gz | 431.9 KB | Display | wwPDB validaton report |
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Full document | 4jkg_full_validation.pdf.gz | 432.8 KB | Display | |
Data in XML | 4jkg_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 4jkg_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/4jkg ftp://data.pdbj.org/pub/pdb/validation_reports/jk/4jkg | HTTPS FTP |
-Related structure data
Related structure data | 4jk7C 4jk8C 4jk9C 4jkaC 4jkbC 4jkcC 4jkdC 4jkeC 4jkfC 4jkhC 3enbS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25452.672 Da / Num. of mol.: 1 / Fragment: PRP8 RNase H-like domain, UNP residues 1769-1990 / Mutation: R1865A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRP8, PRPC8, PRPF8 / Plasmid: pMalC2-E / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta2 / References: UniProt: Q6P2Q9 |
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#2: Protein | Mass: 25448.682 Da / Num. of mol.: 1 / Fragment: PRP8 RNase H-like domain, UNP residues 1769-1990 / Mutation: T1789P, R1865A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRP8, PRPC8, PRPF8 / Plasmid: pMalC2-E / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta2 / References: UniProt: Q6P2Q9 |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Compound details | RESIDUE 1789 IN CHAIN B HAS 2 ALTERNATE IDS THR AND PRO |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.29 % |
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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: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.8→50 Å / Num. obs: 50401 / % possible obs: 94.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.053 / Χ2: 1.001 / Net I/σ(I): 13.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3ENB Resolution: 1.8→40.32 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.2243 / WRfactor Rwork: 0.1858 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8015 / SU B: 2.998 / SU ML: 0.092 / SU R Cruickshank DPI: 0.1364 / SU Rfree: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.13 / 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: 72.91 Å2 / Biso mean: 25.008 Å2 / Biso min: 8.11 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→40.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.844 Å / Total num. of bins used: 20
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