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- PDB-5lsb: Crystal structure of yeast Hsh49p in complex with Cus1p binding d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lsb | ||||||
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Title | Crystal structure of yeast Hsh49p in complex with Cus1p binding domain. | ||||||
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![]() | RNA binding domain / Splicing / U2 snRNP / SF3b complex | ||||||
Function / homology | ![]() U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / positive regulation of mRNA splicing, via spliceosome / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome ...U2-type spliceosomal complex / U2-type prespliceosome assembly / U2 snRNP / positive regulation of mRNA splicing, via spliceosome / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / catalytic step 2 spliceosome / spliceosomal complex / mRNA splicing, via spliceosome / nucleolus / RNA binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | van Roon, A.M. / Obayashi, E. / Sposito, B. / Oubridge, C. / Nagai, K. | ||||||
![]() | ![]() Title: Crystal structure of U2 snRNP SF3b components: Hsh49p in complex with Cus1p-binding domain. Authors: van Roon, A.M. / Oubridge, C. / Obayashi, E. / Sposito, B. / Newman, A.J. / Seraphin, B. / Nagai, K. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 293.6 KB | Display | ![]() |
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PDB format | ![]() | 240.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470 KB | Display | ![]() |
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Full document | ![]() | 474.8 KB | Display | |
Data in XML | ![]() | 25.1 KB | Display | |
Data in CIF | ![]() | 34.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lslSC ![]() 1cvjS 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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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24604.141 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: GGS sequence at the N-terminus is non-natural and left over from TEV-protease cleavage site Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: HSH49, YOR319W, O6142 / Production host: ![]() ![]() #2: Protein | Mass: 9388.993 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Hsh49p binding domain of Cus1p between residues 290-368 Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CUS1, YMR240C, YM9408.02C / Production host: ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.66 % / Description: Thin needles |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Equal volumes of 10-15 mg/ml protein solution were mixed with an equal volume of reservoir solution containing 2.45-2.65 M NaCl in 0.1M sodium acetate pH 4.8-4.9 PH range: 4.8-4.9 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 6, 2007 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 | ||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.7→35.52 Å / Num. obs: 25001 / % possible obs: 99.9 % / Redundancy: 4.2 % / CC1/2: 0.984 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.083 / Rrim(I) all: 0.171 / Net I/σ(I): 13 / Num. measured all: 104708 / Scaling rejects: 11 | ||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LSL, 1CVJ Resolution: 2.7→35.52 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.847 / SU B: 20.317 / SU ML: 0.204 / SU R Cruickshank DPI: 0.3657 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.067 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.82 Å2 / Biso mean: 30.827 Å2 / Biso min: 9.01 Å2
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Refinement step | Cycle: final / Resolution: 2.7→35.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 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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