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Yorodumi- PDB-4bgd: Crystal structure of Brr2 in complex with the Jab1/MPN domain of Prp8 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bgd | ||||||
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Title | Crystal structure of Brr2 in complex with the Jab1/MPN domain of Prp8 | ||||||
Components | (PRE-MRNA-SPLICING ...) x 2 | ||||||
Keywords | TRANSCRIPTION / SPLICEOSOME / RNA HELICASE / U5 SNRNP / RETINITIS PIGMENTOSA | ||||||
Function / homology | Function and homology information spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / generation of catalytic spliceosome for second transesterification step / mRNA 5'-splice site recognition / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly ...spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / generation of catalytic spliceosome for second transesterification step / mRNA 5'-splice site recognition / mRNA 3'-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 / nucleic acid binding / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.1 Å | ||||||
Authors | Nguyen, T.H.D. / Li, J. / Nagai, K. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Structural Basis of Brr2-Prp8 Interactions and Implications for U5 Snrnp Biogenesis and the Spliceosome Active Site Authors: Nguyen, T.H.D. / Li, J. / Galej, W.P. / Oshikane, H. / Newman, A.J. / Nagai, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bgd.cif.gz | 410.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bgd.ent.gz | 323.2 KB | Display | PDB format |
PDBx/mmJSON format | 4bgd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bgd_validation.pdf.gz | 853.3 KB | Display | wwPDB validaton report |
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Full document | 4bgd_full_validation.pdf.gz | 884.2 KB | Display | |
Data in XML | 4bgd_validation.xml.gz | 68.5 KB | Display | |
Data in CIF | 4bgd_validation.cif.gz | 92.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/4bgd ftp://data.pdbj.org/pub/pdb/validation_reports/bg/4bgd | 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
-PRE-MRNA-SPLICING ... , 2 types, 2 molecules AC
#1: Protein | Mass: 195729.453 Da / Num. of mol.: 1 / Fragment: RESIDUES 442-2163 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P32639, RNA helicase |
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#2: Protein | Mass: 28180.924 Da / Num. of mol.: 1 / Fragment: RESIDUES 2148-2395 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: S288C / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P33334 |
-Non-polymers , 4 types, 18 molecules
#3: Chemical | ChemComp-ADP / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-PE5 / |
#6: 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: 3.77 Å3/Da / Density % sol: 67 % Description: THE TWO KNOWN FRAGMENTS COULD ALSO BE FOUND BY MOLECULAR REPLACEMENT, BUT IT WAS NOT SUFFICIENT FOR STRUCTURE DETERMINATION. THE STRUCTURE WAS SOLVED BY SIRAS. |
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Crystal grow | pH: 7.5 / Details: 100 MM HEPESNA PH 7.5, 200 MM MGCL2, 32-40% PEG400 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→92.2 Å / Num. obs: 63788 / % possible obs: 99.9 % / Observed criterion σ(I): 6 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 3.1→3.18 Å / Redundancy: 4 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.4 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: SIRAS Starting model: PDB ENTRIES 3HIB AND 2OG4 Resolution: 3.1→92.37 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.903 / SU B: 19.956 / SU ML: 0.347 / Cross valid method: THROUGHOUT / ESU R Free: 0.436 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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 mean: 121.282 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→92.37 Å
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