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Yorodumi- PDB-4ilg: Crystal structure of Aar2p in complex with the Prp8p RNaseH and J... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ilg | ||||||
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Title | Crystal structure of Aar2p in complex with the Prp8p RNaseH and Jab1/MPN domains | ||||||
Components |
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Keywords | SPLICING / U5 snRNP assembly / Aar2 / Prp8 | ||||||
Function / homology | Function and homology information generation of catalytic spliceosome for second transesterification step / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / pre-mRNA intronic binding ...generation of catalytic spliceosome for second transesterification step / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / metallopeptidase activity / mRNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Weber, G. / Heroven, A.C. / Santos, K.F. / Wahl, M.C. | ||||||
Citation | Journal: Genes Dev. / Year: 2013 Title: Structural basis for dual roles of Aar2p in U5 snRNP assembly. Authors: Weber, G. / Cristao, V.F. / Santos, K.F. / Jovin, S.M. / Heroven, A.C. / Holton, N. / Luhrmann, R. / Beggs, J.D. / Wahl, M.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ilg.cif.gz | 370 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ilg.ent.gz | 299.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ilg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/4ilg ftp://data.pdbj.org/pub/pdb/validation_reports/il/4ilg | HTTPS FTP |
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-Related structure data
Related structure data | 4iliC 4iljC 2og4S 3sbtS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 40219.867 Da / Num. of mol.: 1 / Mutation: Residues 153-170 replaced by 5 Serines Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: AAR2, YBL074C, YBL06.06, YBL0611 / Production host: Escherichia coli (E. coli) / References: UniProt: P32357 |
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#2: Protein | Mass: 29501.113 Da / Num. of mol.: 1 / Fragment: yPrp8 RNaseH (UNP Residues 1835-2090) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C / Production host: Escherichia coli (E. coli) / References: UniProt: P33334 |
#3: Protein | Mass: 30490.338 Da / Num. of mol.: 1 / Fragment: yPrp8 Jab1/MPN (UNP Residues 2147-2413) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: PRP8, DBF3, DNA39, RNA8, SLT21, USA2, YHR165C / Production host: Escherichia coli (E. coli) / References: UniProt: P33334 |
#4: Chemical | ChemComp-EPE / |
#5: 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: 2.97 Å3/Da / Density % sol: 58.53 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES-NaOH, pH 7.5, 12 % (w/v) PEG 6000 and 0.6 M KCl, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 30, 2011 |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→34.3 Å / Num. all: 68910 / Num. obs: 68679 / % possible obs: 99.9 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 1.6 / Redundancy: 3.4 % / Rmerge(I) obs: 0.207 / Rsym value: 0.09 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.1→2.15 Å / % possible obs: 99.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 1.154 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.861 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SBT, 2OG4 Resolution: 2.1→31.869 Å / SU ML: 0.29 / σ(F): 1.99 / Phase error: 23.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.555 Å2 / ksol: 0.291 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→31.869 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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