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Open data
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Basic information
Entry | Database: PDB / ID: 5cyz | ||||||
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Title | Structure of S. cerevisiae Hrr25:Mam1 complex, form 1 | ||||||
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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 | ![]() | 222.3 KB | Display | ![]() |
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PDB format | ![]() | 176.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.7 KB | Display | ![]() |
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Full document | ![]() | 450.8 KB | Display | |
Data in XML | ![]() | 23.2 KB | Display | |
Data in CIF | ![]() | 32.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xh0C ![]() 4xhgC ![]() 4xhhC ![]() 4xhlSC ![]() 5czoC 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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Unit cell |
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Components
#1: Protein | Mass: 46438.375 Da / Num. of mol.: 1 / Mutation: K38R, N-terminal Ala from tag 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 |
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#2: Protein | Mass: 12903.680 Da / Num. of mol.: 1 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 | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.9 Details: 0.1M CHES pH8.9, 5% Tacsimate, 25 mM YCl3, 19% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→48.2 Å / Num. obs: 48597 / % possible obs: 99 % / Redundancy: 6.1 % / Rsym value: 0.152 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.4 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4XHL Resolution: 1.841→48.2 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.96 / 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: 1.841→48.2 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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