+Open data
-Basic information
Entry | Database: PDB / ID: 6yie | ||||||
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Title | Structure of a Borealin-INCENP-Survivin complex | ||||||
Components |
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Keywords | CELL CYCLE | ||||||
Function / homology | Function and homology information 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 / mitotic metaphase chromosome alignment / cysteine-type endopeptidase inhibitor activity / cobalt ion binding / 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 / 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 / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / pericentric heterochromatin / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / centriole / positive regulation of mitotic cell cycle / tubulin binding / molecular function activator activity / chromosome segregation / RHO GTPases Activate Formins / sensory perception of sound / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / spindle microtubule / kinetochore / small GTPase binding / spindle / Separation of Sister Chromatids / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / Neddylation / mitotic cell cycle / midbody / protein-folding chaperone binding / microtubule binding / Interleukin-4 and Interleukin-13 signaling / microtubule / nuclear body / protein heterodimerization activity / cell division / protein phosphorylation / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of cell population proliferation / nucleolus / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å | ||||||
Authors | Serena, M. / Elliott, P.R. / Barr, F.A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Cell Biol. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yie.cif.gz | 318.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yie.ent.gz | 219.2 KB | Display | PDB format |
PDBx/mmJSON format | 6yie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/6yie ftp://data.pdbj.org/pub/pdb/validation_reports/yi/6yie | HTTPS FTP |
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-Related structure data
Related structure data | 6yifC 6yihC 6yipC 2qfaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 16568.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC5, API4, IAP4 / Plasmid: pETDuet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus (RIL) / References: UniProt: O15392 #2: Protein | Mass: 11617.326 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDCA8, PESCRG3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus (RIL) / References: UniProt: Q53HL2 #3: Protein | Mass: 7018.110 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INCENP / Plasmid: PFAT2-His6-GST / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus (RIL) / References: UniProt: Q9NQS7 #4: Chemical | Has ligand of interest | N | |
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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: 2.09 Å3/Da / Density % sol: 41.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 5 % (w/v) PEG 3,350, 50 mM MES pH 6.0 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 3.49→78.82 Å / Num. obs: 6947 / % possible obs: 88.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 65.27 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.162 / Net I/σ(I): 3.5 |
Reflection shell | Resolution: 3.49→3.83 Å / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1644 / CC1/2: 0.902 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QFA Resolution: 3.49→66.7 Å / SU ML: 0.4279 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.3698
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.49→66.7 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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