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Yorodumi- PDB-2qjz: Structural Basis of Microtubule Plus End Tracking by XMAP215, CLI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qjz | ||||||
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Title | Structural Basis of Microtubule Plus End Tracking by XMAP215, CLIP-170 and EB1 | ||||||
Components | Microtubule-associated protein RP/EB family member 1 | ||||||
Keywords | PROTEIN BINDING / EB1 / calponin homology domain / microtubule plus end / +TIP | ||||||
Function / homology | Function and homology information protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / non-motile cilium assembly / microtubule bundle formation ...protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / non-motile cilium assembly / microtubule bundle formation / protein localization to centrosome / microtubule organizing center / negative regulation of microtubule polymerization / mitotic spindle pole / microtubule polymerization / establishment of mitotic spindle orientation / regulation of microtubule polymerization or depolymerization / spindle midzone / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule / Mitotic Prometaphase / spindle assembly / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / positive regulation of microtubule polymerization / AURKA Activation by TPX2 / ciliary basal body / RHO GTPases Activate Formins / protein localization / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / cell migration / microtubule / molecular adaptor activity / cadherin binding / cell division / focal adhesion / centrosome / protein kinase binding / Golgi apparatus / RNA binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.25 Å | ||||||
Authors | Slep, K.C. / Vale, R.D. | ||||||
Citation | Journal: Mol.Cell / Year: 2007 Title: Structural Basis of Microtubule Plus End Tracking by XMAP215, CLIP-170, and EB1. Authors: Slep, K.C. / Vale, R.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qjz.cif.gz | 115.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qjz.ent.gz | 94.3 KB | Display | PDB format |
PDBx/mmJSON format | 2qjz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/2qjz ftp://data.pdbj.org/pub/pdb/validation_reports/qj/2qjz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological assembly is a dimer formed by a conserved C-terminal coiled-coil / four helix bundle dimerization domain not included in this construct. |
-Components
#1: Protein | Mass: 14455.015 Da / Num. of mol.: 2 / Fragment: Calponin Homology Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPRE1 / Plasmid: pGEX-6P2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: Q15691 #2: 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: 2.07 Å3/Da / Density % sol: 40.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 11.5% 2-propanol, 190 mM Sodium citrate, 100 mM Hepes, Protein concentration 20 mg/ml, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9798, 1.1271, 0.7999 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 10, 2001 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Χ2: 0.99 / D res low: 50 Å
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Diffraction reflection shell |
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Reflection | Resolution: 1.25→50 Å / Num. obs: 63420 / % possible obs: 97.4 % / Rmerge(I) obs: 0.054 / Rsym value: 5.4 / Χ2: 0.97 / Net I/σ(I): 13.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.25→1.29 Å / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5181 / Rsym value: 32.1 / Χ2: 0.941 / % possible all: 95.7 |
-Phasing
Phasing | Method: MAD |
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Phasing dm shell | Resolution: 1.6→500.01 Å / Delta phi final: 0.123 / FOM : 0.126 / Reflection: 51131 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.25→45.22 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.382 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.052 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.271 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→45.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.282 Å / Total num. of bins used: 20
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