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- PDB-6yif: Structure of Chromosomal Passenger Complex (CPC) bound to phospho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6yif | ||||||
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Title | Structure of Chromosomal Passenger Complex (CPC) bound to phosphorylated Histone 3 peptide at 1.8 A. | ||||||
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![]() | CELL CYCLE | ||||||
Function / homology | ![]() central element / meiotic spindle midzone / survivin complex / meiotic spindle midzone assembly / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / positive regulation of exit from mitosis / positive regulation of mitotic cell cycle spindle assembly checkpoint ...central element / meiotic spindle midzone / survivin complex / meiotic spindle midzone assembly / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / positive regulation of exit from mitosis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / chromocenter / interphase microtubule organizing center / lateral element / protein-containing complex localization / chromosome passenger complex / cysteine-type endopeptidase inhibitor activity / mitotic metaphase chromosome alignment / nuclear chromosome / intercellular bridge / mitotic spindle assembly checkpoint signaling / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / cobalt ion binding / cytoplasmic microtubule / mitotic sister chromatid segregation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / SUMOylation of DNA replication proteins / chromosome, centromeric region / mitotic cytokinesis / mitotic spindle assembly / chromosome organization / spindle midzone / Chromatin modifying enzymes / pericentric heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / epigenetic regulation of gene expression / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / telomere organization / centriole / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / tubulin binding / positive regulation of mitotic cell cycle / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / molecular function activator activity / chromosome segregation / HDACs deacetylate histones / RHO GTPases Activate Formins / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / sensory perception of sound / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / spindle microtubule / PKMTs methylate histone lysines / Meiotic recombination / kinetochore / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / small GTPase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / spindle / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / Separation of Sister Chromatids / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / mitotic cell cycle / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / midbody / protein-folding chaperone binding / Senescence-Associated Secretory Phenotype (SASP) / microtubule binding / Interleukin-4 and Interleukin-13 signaling / Oxidative Stress Induced Senescence / microtubule Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Serena, M. / Elliott, P.R. / Barr, F.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis of MKLP2-dependent Aurora B transport from chromatin to the anaphase central spindle. Authors: Serena, M. / Bastos, R.N. / Elliott, P.R. / Barr, F.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 186.4 KB | Display | ![]() |
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PDB format | ![]() | 124.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.9 KB | Display | ![]() |
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Full document | ![]() | 468.9 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6yieC ![]() 6yihC ![]() 6yipC ![]() 2qfaS 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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Unit cell |
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Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 16568.902 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 8164.490 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 6176.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules D
#4: Protein/peptide | Mass: 1388.468 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 3 types, 232 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-ZN / | ||
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#6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.31 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.5 Details: 20 % (w/v) PEG 4,000, 200 mM Lithium sulphate, 50 mM MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96859 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→49.43 Å / Num. obs: 28454 / % possible obs: 99.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 25.37 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.81→1.86 Å / Rmerge(I) obs: 0.953 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2126 / CC1/2: 0.544 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2QFA Resolution: 1.81→49.43 Å / SU ML: 0.1901 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.8182
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→49.43 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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