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Yorodumi- PDB-1pa7: Crystal structure of amino-terminal microtubule binding domain of EB1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pa7 | ||||||
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Title | Crystal structure of amino-terminal microtubule binding domain of EB1 | ||||||
Components | Microtubule-associated protein RP/EB family member 1 | ||||||
Keywords | STRUCTURAL PROTEIN / CH domain | ||||||
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 assembly / spindle midzone / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of microtubule polymerization / 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 / 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: 1.45 Å | ||||||
Authors | Hayashi, I. / Ikura, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Crystal structure of the amino-terminal microtubule-binding domain of end-binding protein 1 (EB1) Authors: Hayashi, I. / Ikura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pa7.cif.gz | 41.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pa7.ent.gz | 28.9 KB | Display | PDB format |
PDBx/mmJSON format | 1pa7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/1pa7 ftp://data.pdbj.org/pub/pdb/validation_reports/pa/1pa7 | HTTPS FTP |
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-Related 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: 15050.383 Da / Num. of mol.: 1 / Fragment: N-terminal domain, EB1 microtubule-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EB1 (amino acids 1-130) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15691 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.12 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PEG4K, ammonium sulfate, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 7, 2002 / Details: mirror |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→20 Å / Num. obs: 23798 / Rmerge(I) obs: 0.042 |
Reflection shell | Resolution: 1.45→1.5 Å / Rmerge(I) obs: 0.228 / Num. unique all: 2278 |
Reflection | *PLUS % possible obs: 99 % |
Reflection shell | *PLUS % possible obs: 97.8 % / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 6.99 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.45→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 0.932 / SU ML: 0.037 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.064 / 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: 12.199 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.448→1.486 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Origin x: 2.8131 Å / Origin y: 23.293 Å / Origin z: 32.6876 Å
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Refinement | *PLUS Num. reflection obs: 21093 / % reflection Rfree: 5 % / Rfactor Rfree: 0.189 / Rfactor Rwork: 0.173 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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