+Open data
-Basic information
Entry | Database: PDB / ID: 3hkb | ||||||
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Title | Tubulin: RB3 Stathmin-like domain complex | ||||||
Components |
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Keywords | CELL CYCLE / ALPHA-TUBULIN / BETA-TUBULIN / GTPASE / MICROTUBULE / STATHMIN / TUBULIN | ||||||
Function / homology | Function and homology information axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior ...axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior / microtubule depolymerization / response to L-glutamate / smoothened signaling pathway / regulation of synapse organization / startle response / locomotory exploration behavior / microtubule polymerization / regulation of microtubule polymerization or depolymerization / response to tumor necrosis factor / response to mechanical stimulus / condensed chromosome / homeostasis of number of cells within a tissue / cellular response to calcium ion / tubulin binding / adult locomotory behavior / intracellular protein transport / synapse organization / neuron migration / visual learning / neuromuscular junction / recycling endosome / structural constituent of cytoskeleton / memory / cerebral cortex development / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / neuron projection development / mitotic cell cycle / gene expression / growth cone / neuron apoptotic process / microtubule / hydrolase activity / neuron projection / protein heterodimerization activity / GTPase activity / protein-containing complex binding / GTP binding / Golgi apparatus / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Ovis aries (sheep) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.65 Å | ||||||
Authors | Dorleans, A. / Gigant, B. / Ravelli, R.B.G. / Mailliet, P. / Mikol, V. / Knossow, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Variations in the colchicine-binding domain provide insight into the structural switch of tubulin Authors: Dorleans, A. / Gigant, B. / Ravelli, R.B.G. / Mailliet, P. / Mikol, V. / Knossow, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hkb.cif.gz | 358 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hkb.ent.gz | 282.4 KB | Display | PDB format |
PDBx/mmJSON format | 3hkb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/3hkb ftp://data.pdbj.org/pub/pdb/validation_reports/hk/3hkb | HTTPS FTP |
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-Related structure data
Related structure data | 3hkcC 3hkdC 3hkeC 1sa0S 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
-Protein , 3 types, 5 molecules ACBDE
#1: Protein | Mass: 50188.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: brain / References: UniProt: D0VWZ0*PLUS #2: Protein | Mass: 49969.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: brain / References: UniProt: D0VWY9*PLUS #3: Protein | | Mass: 16712.967 Da / Num. of mol.: 1 / Fragment: RB3 stathmin-like domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Plasmid: PET-8C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63043 |
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-Non-polymers , 3 types, 6 molecules
#4: Chemical | #5: Chemical | #6: Chemical | |
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-Details
Sequence details | THERE IS ONE COMPLEX IN THE ASYMMETRIC UNIT, WHICH CONSISTS OF TWO ALPHA-BETA TUBULIN HETERODIMERS ...THERE IS ONE COMPLEX IN THE ASYMMETRIC |
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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: 3.86 Å3/Da / Density % sol: 68 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG, PIPES BUFFER, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.978 / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2006 |
Radiation | Monochromator: CHANNEL CUT ESRF MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 3.65→25 Å / Num. all: 37976 / Num. obs: 36513 / % possible obs: 96.4 % / Redundancy: 3.1 % / Rsym value: 0.055 / Net I/σ(I): 19 |
Reflection shell | Resolution: 3.65→3.73 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.28 / Rsym value: 0.442 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SA0 Resolution: 3.65→20 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.896 / SU B: 34.51 / SU ML: 0.499 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.61 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 61.974 Å2
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Refinement step | Cycle: LAST / Resolution: 3.65→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.65→3.742 Å / Total num. of bins used: 20 /
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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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