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- PDB-7b1f: Orthorhombic P212121 Structure of Human Mad1 C-terminal Domain in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7b1f | |||||||||
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Title | Orthorhombic P212121 Structure of Human Mad1 C-terminal Domain in Complex with Phosphorylated Bub1 CD1 Domain | |||||||||
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![]() | CELL CYCLE / mad1 / bub1 / mitotic checkpoint complex / spindle assembly checkpoint | |||||||||
Function / homology | ![]() MAD1 complex / histone H2A kinase activity / positive regulation of maintenance of mitotic sister chromatid cohesion, centromeric / deactivation of mitotic spindle assembly checkpoint / mitotic spindle assembly checkpoint MAD1-MAD2 complex / regulation of sister chromatid cohesion / regulation of chromosome segregation / positive regulation of mitotic cell cycle spindle assembly checkpoint / regulation of metaphase plate congression / meiotic sister chromatid cohesion, centromeric ...MAD1 complex / histone H2A kinase activity / positive regulation of maintenance of mitotic sister chromatid cohesion, centromeric / deactivation of mitotic spindle assembly checkpoint / mitotic spindle assembly checkpoint MAD1-MAD2 complex / regulation of sister chromatid cohesion / regulation of chromosome segregation / positive regulation of mitotic cell cycle spindle assembly checkpoint / regulation of metaphase plate congression / meiotic sister chromatid cohesion, centromeric / cytoplasmic sequestering of protein / kinetochore binding / nuclear pore nuclear basket / outer kinetochore / attachment of mitotic spindle microtubules to kinetochore / mitotic spindle assembly checkpoint signaling / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / negative regulation of T cell proliferation / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / thymus development / chromosome segregation / RHO GTPases Activate Formins / mitotic spindle / kinetochore / spindle pole / spindle / Separation of Sister Chromatids / nuclear envelope / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / cell division / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Fischer, E. / Bellini, D. / Barford, D. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular mechanism of Mad1 kinetochore targeting by phosphorylated Bub1. Authors: Fischer, E.S. / Yu, C.W.H. / Bellini, D. / McLaughlin, S.H. / Orr, C.M. / Wagner, A. / Freund, S.M.V. / Barford, D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.3 KB | Display | ![]() |
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PDB format | ![]() | 54.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.9 KB | Display | ![]() |
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Full document | ![]() | 476.6 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7b1hC ![]() 7b1jC ![]() 4dzoS 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: 13961.832 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 3023.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() References: UniProt: O43683, non-specific serine/threonine protein kinase #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 4000, 0.1 M Hepes pH 7.5, 10% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→40.25 Å / Num. obs: 33937 / % possible obs: 89 % / Redundancy: 5.6 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.02 / Rrim(I) all: 0.06 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.75→1.813 Å / Rmerge(I) obs: 1.97 / Num. unique obs: 1863 / CC1/2: 0.3 / Rpim(I) all: 1.2 / Rrim(I) all: 2.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DZO Resolution: 1.75→40.25 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 37.2 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 147.96 Å2 / Biso mean: 56.9543 Å2 / Biso min: 23.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→40.25 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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