+Open data
-Basic information
Entry | Database: PDB / ID: 6yip | ||||||
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Title | Structure of MKLP2 coiled coil | ||||||
Components | Kinesin-like protein KIF20AKIF20A | ||||||
Keywords | CELL CYCLE | ||||||
Function / homology | Function and homology information microtubule motor activity => GO:0003777 / Mitotic Telophase/Cytokinesis / midbody abscission / microtubule bundle formation / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / intercellular bridge / microtubule-based movement ...microtubule motor activity => GO:0003777 / Mitotic Telophase/Cytokinesis / midbody abscission / microtubule bundle formation / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / intercellular bridge / microtubule-based movement / cleavage furrow / mitotic cytokinesis / MHC class II antigen presentation / regulation of cytokinesis / spindle / protein transport / midbody / microtubule binding / microtubule / protein kinase binding / Golgi apparatus / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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 | 6yip.cif.gz | 112.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yip.ent.gz | 71.6 KB | Display | PDB format |
PDBx/mmJSON format | 6yip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/6yip ftp://data.pdbj.org/pub/pdb/validation_reports/yi/6yip | HTTPS FTP |
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-Related structure data
Related structure data | 6yieC 6yifC 6yihC 5lefS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9076.976 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIF20A, MKLP2, RAB6KIFL / Plasmid: pFAT2 His6-GST / Cell (production host): BL21 CodonPlus (DE3) RIL / Production host: Escherichia coli (E. coli) / References: UniProt: O95235 #2: Chemical | ChemComp-IPA / | #3: Water | ChemComp-HOH / | 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: 2.46 Å3/Da / Density % sol: 50.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 5.6 Details: 20% (w/v) PEG 4,000, 20 % (v/v) 2-propanol, 100 mM sodium citrate, pH 5.6. |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→79.87 Å / Num. obs: 11058 / % possible obs: 87.9 % / Redundancy: 13.7 % / Biso Wilson estimate: 13.58 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.162 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.43→1.66 Å / Rmerge(I) obs: 1.486 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 554 / CC1/2: 0.854 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LEF Resolution: 1.43→32.25 Å / SU ML: 0.2171 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 45.1804
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→32.25 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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