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Open data
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Basic information
Entry | Database: PDB / ID: 5czo | ||||||
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Title | Structure of S. cerevisiae Hrr25:Mam1 complex, form 2 | ||||||
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![]() | TRANSFERASE / casein kinase / monopolin | ||||||
Function / homology | ![]() meiotic sister chromatid cohesion involved in meiosis I / regulation of vesicle fusion with Golgi apparatus / regulation of protein localization by the Cvt pathway / monopolin complex / positive regulation of clathrin-dependent endocytosis / spindle attachment to meiosis I kinetochore / regulation of ER to Golgi vesicle-mediated transport / meiotic chromosome segregation / COPII-mediated vesicle transport / tRNA wobble uridine modification ...meiotic sister chromatid cohesion involved in meiosis I / regulation of vesicle fusion with Golgi apparatus / regulation of protein localization by the Cvt pathway / monopolin complex / positive regulation of clathrin-dependent endocytosis / spindle attachment to meiosis I kinetochore / regulation of ER to Golgi vesicle-mediated transport / meiotic chromosome segregation / COPII-mediated vesicle transport / tRNA wobble uridine modification / homologous chromosome segregation / cellular bud tip / regulation of autophagosome assembly / pexophagy / cellular bud neck / spindle pole body / preribosome, small subunit precursor / chromosome, centromeric region / spindle assembly / ribosomal large subunit biogenesis / spindle microtubule / regulation of circadian rhythm / kinetochore / endocytosis / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / ribosomal small subunit biogenesis / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ye, Q. / Corbett, K.D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the Saccharomyces cerevisiae Hrr25:Mam1 monopolin subcomplex reveals a novel kinase regulator. Authors: Ye, Q. / Ur, S.N. / Su, T.Y. / Corbett, K.D. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 413 KB | Display | ![]() |
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PDB format | ![]() | 341.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.6 KB | Display | ![]() |
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Full document | ![]() | 476.4 KB | Display | |
Data in XML | ![]() | 34.3 KB | Display | |
Data in CIF | ![]() | 45.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xh0C ![]() 4xhgC ![]() 4xhhC ![]() 4xhlSC ![]() 5cyzC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 46249.059 Da / Num. of mol.: 2 / Mutation: K38R Source method: isolated from a genetically manipulated source Details: surface LYS residues methylated (MLY) Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: HRR25, YPL204W / Production host: ![]() ![]() References: UniProt: P29295, non-specific serine/threonine protein kinase #2: Protein | Mass: 12876.634 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: surface LYS residues methylated (MLY) Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: MAM1, YER106W / Production host: ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Imidazole pH 8.0, 14% PEG3350, 6% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2829 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→132.4 Å / % possible obs: 99.8 % / Redundancy: 3.5 % / Rsym value: 0.112 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.36 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XHL Resolution: 2.894→49.692 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 30.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.894→49.692 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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