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Yorodumi- PDB-2qyf: Crystal structure of the Mad2/p31(comet)/Mad2-binding peptide ter... -
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-Basic information
Entry | Database: PDB / ID: 2qyf | ||||||
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Title | Crystal structure of the Mad2/p31(comet)/Mad2-binding peptide ternary complex | ||||||
Components |
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Keywords | CELL CYCLE / PROTEIN-PEPTIDE COMPLEX / MAD2 FAMILY / SPINDLE ASSEMBLY CHECKPOINT / Cell division / Mitosis / Nucleus / Phosphorylation | ||||||
Function / homology | Function and homology information deactivation of mitotic spindle assembly checkpoint / mitotic spindle assembly checkpoint MAD1-MAD2 complex / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of mitotic cell cycle spindle assembly checkpoint / establishment of centrosome localization / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / regulation of exit from mitosis / nuclear pore nuclear basket ...deactivation of mitotic spindle assembly checkpoint / mitotic spindle assembly checkpoint MAD1-MAD2 complex / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of mitotic cell cycle spindle assembly checkpoint / establishment of centrosome localization / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / regulation of exit from mitosis / nuclear pore nuclear basket / negative regulation of ubiquitin protein ligase activity / mitotic spindle assembly checkpoint signaling / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / negative regulation of mitotic cell cycle / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / APC-Cdc20 mediated degradation of Nek2A / RHO GTPases Activate Formins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / negative regulation of protein catabolic process / mitotic spindle / kinetochore / spindle pole / spindle / Separation of Sister Chromatids / nuclear membrane / cell division / nucleolus / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Tomchick, D.R. / Luo, X. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2007 Title: p31comet blocks Mad2 activation through structural mimicry. Authors: Yang, M. / Li, B. / Tomchick, D.R. / Machius, M. / Rizo, J. / Yu, H. / Luo, X. #1: Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: The Mad2 spindle checkpoint protein has two distinct natively folded states. Authors: Luo, X. / Tang, Z. / Xia, G. / Wassmann, K. / Matsumoto, T. / Rizo, J. / Yu, H. #2: Journal: Mol.Cell / Year: 2002 Title: The Mad2 Spindle Checkpoint Protein Undergoes Similar Major Conformational Changes Upon Binding to Either Mad1 or Cdc20 Authors: Luo, X. / Tang, Z. / Rizo, J. / Yu, H. #3: Journal: Nat.Struct.Mol.Biol. / Year: 2000 Title: Structure of the Mad2 spindle assembly checkpoint protein and its interaction with Cdc20. Authors: Luo, X. / Fang, G. / Coldiron, M. / Lin, Y. / Yu, H. / Kirschner, M.W. / Wagner, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qyf.cif.gz | 179.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qyf.ent.gz | 147.7 KB | Display | PDB format |
PDBx/mmJSON format | 2qyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qyf_validation.pdf.gz | 464.5 KB | Display | wwPDB validaton report |
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Full document | 2qyf_full_validation.pdf.gz | 472.1 KB | Display | |
Data in XML | 2qyf_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 2qyf_validation.cif.gz | 54 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/2qyf ftp://data.pdbj.org/pub/pdb/validation_reports/qy/2qyf | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23595.750 Da / Num. of mol.: 2 / Mutation: L13A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAD2L1, MAD2 / Plasmid: pETDuet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13257 #2: Protein | Mass: 27687.914 Da / Num. of mol.: 2 / Fragment: UNP residues 36-274 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAD2L1BP, CMT2, KIAA0110 / Plasmid: pETDuet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15013 #3: Protein/peptide | Mass: 1451.604 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic 12-mer #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.99 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 16% (w/v) PEG 3350, 16% (v/v) glycerol, 125 mM sodium phosphate (pH 5.0), 100 mM NaCl, 25 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2005 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97912 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→44.23 Å / Num. all: 44434 / Num. obs: 44434 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 4 / Num. unique all: 2216 / Rsym value: 0.621 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.894 / SU B: 6.432 / SU ML: 0.16 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.306 / ESU R Free: 0.245 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.962 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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