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Open data
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Basic information
Entry | Database: PDB / ID: 5j2u | ||||||||||||
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Title | Tubulin-MMAF complex | ||||||||||||
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![]() | CELL CYCLE / CYTOSKELETON / TUBULIN FOLD / MICROTUBULE | ||||||||||||
Function / homology | ![]() tubulin-tyrosine ligase / tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process ...tubulin-tyrosine ligase / tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / mitotic cell cycle / nervous system development / growth cone / microtubule / neuron projection / protein heterodimerization activity / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() synthetic construct (others) | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Waight, A.B. / Bargsten, K. / Doronina, S. / Steinmetz, M.O. / Sussman, D. / Prota, A.E. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis of Microtubule Destabilization by Potent Auristatin Anti-Mitotics. Authors: Waight, A.B. / Bargsten, K. / Doronina, S. / Steinmetz, M.O. / Sussman, D. / Prota, A.E. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 837.8 KB | Display | ![]() |
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PDB format | ![]() | 691.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5iyzC ![]() 5j2tC ![]() 4i4tS 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 , 2 types, 3 molecules ACE
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | | Mass: 16844.162 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Tubulin beta-2B ... , 2 types, 3 molecules BDF
#2: Protein | Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | | Mass: 44378.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Protein/peptide , 1 types, 2 molecules GH
#5: Protein/peptide | Mass: 731.962 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 6 types, 149 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/ACP.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Chemical | ChemComp-MG / #8: Chemical | ChemComp-CA / | #9: Chemical | #10: Chemical | ChemComp-ACP / | #11: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 5% PEG, 12% glycerol, 30 mM magnesium chloride, 30 mM calcium chloride, 0.1M MES/0.1M imidazole |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: NOIR-1 / Detector: CCD / Date: Oct 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→56.654 Å / Num. obs: 102228 / % possible obs: 99 % / Redundancy: 6.9 % / Rsym value: 0.152 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 0.8 / Rsym value: 2.059 / % possible all: 93.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4I4T Resolution: 2.5→56.654 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.14
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→56.654 Å
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Refine LS restraints |
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LS refinement shell |
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