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Open data
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Basic information
Entry | Database: PDB / ID: 3ryf | ||||||
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Title | GTP-Tubulin: RB3 Stathmin-like domain complex | ||||||
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![]() | CELL CYCLE / ALPHA-TUBULIN / BETA-TUBULIN / GTP / GTPASE / MICROTUBULE / STATHMIN S-TUBULIN / SUBTILISIN / TUBULIN | ||||||
Function / homology | ![]() 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 / synapse organization / intracellular protein transport / neuron migration / visual learning / neuromuscular junction / recycling endosome / structural constituent of cytoskeleton / cerebral cortex development / memory / cytoplasmic ribonucleoprotein granule / microtubule cytoskeleton organization / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nawrotek, A. / Knossow, M. / Gigant, B. | ||||||
![]() | ![]() Title: The Determinants That Govern Microtubule Assembly from the Atomic Structure of GTP-Tubulin. Authors: Nawrotek, A. / Knossow, M. / Gigant, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 774 KB | Display | ![]() |
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PDB format | ![]() | 639.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 72 KB | Display | |
Data in CIF | ![]() | 97.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3rycC ![]() 3ryhC ![]() 3ryiC ![]() 3hkbS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 3 types, 5 molecules ACBDE
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 50043.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | | Mass: 16745.975 Da / Num. of mol.: 1 / Fragment: Residues 48-189 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 379 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GTP / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | AUTHOR STATES THAT FOR ALPHA-TUBULIN (CHAIN A AND CHAIN C), THE BOVINE BRAIN TUBULIN SEQUENCE WAS ...AUTHOR STATES THAT FOR ALPHA-TUBULIN (CHAIN A AND CHAIN C), THE BOVINE BRAIN TUBULIN SEQUENCE WAS USED FOR REFINEMENT |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: PEG, LISO4, PIPES BUFFER, pH 6.80, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→42.7 Å / Num. obs: 71650 / % possible obs: 99.3 % / Redundancy: 4 % / Biso Wilson estimate: 60.44 Å2 / Rsym value: 0.097 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.52→2.58 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.84 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3HKB Resolution: 2.52→36.9 Å / Cor.coef. Fo:Fc: 0.9519 / Cor.coef. Fo:Fc free: 0.9278 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 71.07 Å2
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Refine analyze | Luzzati coordinate error obs: 0.346 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.52→36.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.52→2.58 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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