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Yorodumi- PDB-3uai: Structure of the Shq1-Cbf5-Nop10-Gar1 complex from Saccharomyces ... -
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-Basic information
Entry | Database: PDB / ID: 3uai | ||||||
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Title | Structure of the Shq1-Cbf5-Nop10-Gar1 complex from Saccharomyces cerevisiae | ||||||
Components |
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Keywords | ISOMERASE/CHAPERONE / H/ACA RNP assembly intermediate / H/ACA RNA / Nuclear / ISOMERASE-CHAPERONE complex | ||||||
Function / homology | Function and homology information snRNA pseudouridine synthase activity / Telomere Extension By Telomerase / box H/ACA snoRNP assembly / snoRNA guided rRNA pseudouridine synthesis / box H/ACA snoRNP complex / Isomerases; Intramolecular transferases; Transferring other groups / rRNA pseudouridine synthesis / box H/ACA sno(s)RNA 3'-end processing / snRNA pseudouridine synthesis / box H/ACA snoRNA binding ...snRNA pseudouridine synthase activity / Telomere Extension By Telomerase / box H/ACA snoRNP assembly / snoRNA guided rRNA pseudouridine synthesis / box H/ACA snoRNP complex / Isomerases; Intramolecular transferases; Transferring other groups / rRNA pseudouridine synthesis / box H/ACA sno(s)RNA 3'-end processing / snRNA pseudouridine synthesis / box H/ACA snoRNA binding / mRNA pseudouridine synthesis / pseudouridine synthase activity / rRNA modification / sno(s)RNA-containing ribonucleoprotein complex / telomerase RNA binding / snoRNA binding / chromosome, centromeric region / 90S preribosome / rRNA processing / unfolded protein binding / microtubule / cell division / mRNA binding / nucleolus / DNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å | ||||||
Authors | Ye, K. | ||||||
Citation | Journal: Embo J. / Year: 2011 Title: Structure of the Shq1-Cbf5-Nop10-Gar1 complex and implications for H/ACA RNP biogenesis and dyskeratosis congenita Authors: Li, S. / Duan, J. / Li, D. / Ma, S. / Ye, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uai.cif.gz | 346.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uai.ent.gz | 285.8 KB | Display | PDB format |
PDBx/mmJSON format | 3uai.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uai_validation.pdf.gz | 456.6 KB | Display | wwPDB validaton report |
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Full document | 3uai_full_validation.pdf.gz | 469.8 KB | Display | |
Data in XML | 3uai_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 3uai_validation.cif.gz | 40 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/3uai ftp://data.pdbj.org/pub/pdb/validation_reports/ua/3uai | HTTPS FTP |
-Related structure data
Related structure data | 3uahSC 3u28S 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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Unit cell |
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-Components
#1: Protein | Mass: 44981.797 Da / Num. of mol.: 1 / Fragment: Core domain, UNP residues 3-394 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288c / Gene: CBF5 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) References: UniProt: P33322, Isomerases; Intramolecular transferases; Transferring other groups |
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#2: Protein | Mass: 6649.745 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288c / Gene: NOP10 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q6Q547 |
#3: Protein | Mass: 12618.431 Da / Num. of mol.: 1 / Fragment: Core domain, UNP residues 32-124 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288c / Gene: GAR1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P28007 |
#4: Protein | Mass: 42928.047 Da / Num. of mol.: 1 / Fragment: Shq1 specific domain, UNP residues 147-504 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288c / Gene: SHQ1 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P40486 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.03 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Bis-Tris, 20%(w/v) polyethylene glycol monomethyl ether 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å |
Detector | Detector: CCD / Date: Jun 6, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 3.06→50 Å / Num. obs: 27487 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 58.4 |
Reflection shell | Resolution: 3.06→3.11 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 5.6 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UAH, 3U28 Resolution: 3.06→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.907 / SU B: 37.907 / SU ML: 0.311 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.434 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 100.637 Å2
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Refinement step | Cycle: LAST / Resolution: 3.06→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.062→3.14 Å / Total num. of bins used: 20
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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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