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- PDB-6j4v: Structural basis of tubulin detyrosination by vasohibins-SVBP enz... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6j4v | ||||||||||||
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Title | Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications | ||||||||||||
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![]() | HYDROLASE / carboxypeptidase / tubulin / microtubule. | ||||||||||||
Function / homology | ![]() cell-cell fusion / regulation of metallopeptidase activity / syncytium formation by plasma membrane fusion / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Post-chaperonin tubulin folding pathway / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Carboxyterminal post-translational modifications of tubulin / peptidase activator activity ...cell-cell fusion / regulation of metallopeptidase activity / syncytium formation by plasma membrane fusion / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Post-chaperonin tubulin folding pathway / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Carboxyterminal post-translational modifications of tubulin / peptidase activator activity / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / cytoskeleton-dependent intracellular transport / Formation of tubulin folding intermediates by CCT/TriC / Gap junction assembly / COPI-independent Golgi-to-ER retrograde traffic / Assembly and cell surface presentation of NMDA receptors / Kinesins / negative regulation of endothelial cell migration / labyrinthine layer blood vessel development / COPI-dependent Golgi-to-ER retrograde traffic / axon development / cytoplasmic microtubule / Recycling pathway of L1 / microtubule-based process / RHOH GTPase cycle / protein secretion / RHO GTPases activate IQGAPs / cellular response to interleukin-4 / regulation of angiogenesis / Hedgehog 'off' state / COPI-mediated anterograde transport / metallocarboxypeptidase activity / Activation of AMPK downstream of NMDARs / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / negative regulation of protein ubiquitination / Recruitment of NuMA to mitotic centrosomes / positive regulation of endothelial cell proliferation / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / PKR-mediated signaling / structural constituent of cytoskeleton / microtubule cytoskeleton organization / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / positive regulation of angiogenesis / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / double-stranded RNA binding / apical part of cell / mitotic cell cycle / actin binding / microtubule binding / microtubule / cytoskeleton / cell division / GTPase activity / ubiquitin protein ligase binding / GTP binding / structural molecule activity / proteolysis / extracellular region / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Wang, N. / Bao, H. / Huang, H. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of tubulin detyrosination by the vasohibin-SVBP enzyme complex. Authors: Wang, N. / Bosc, C. / Ryul Choi, S. / Boulan, B. / Peris, L. / Olieric, N. / Bao, H. / Krichen, F. / Chen, L. / Andrieux, A. / Olieric, V. / Moutin, M.J. / Steinmetz, M.O. / Huang, H. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 142.1 KB | Display | ![]() |
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PDB format | ![]() | 109.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6j4oSC ![]() 6j4pC ![]() 6j4qC ![]() 6j4sC ![]() 6j4uC ![]() 6qbyC S: Starting model for refinement C: citing same article ( |
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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 on special symmetry positions |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 29322.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 7805.874 Da / Num. of mol.: 1 / Mutation: C58S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 2323.269 Da / Num. of mol.: 1 / Mutation: E450C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 3 types, 245 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.32 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 8.2 Details: For crystallization of V2c-SVBP C58S in complex with the maTail peptide the components were mixed in a 1:3 molar ratio and incubated at room temperature for 24 h before setting up ...Details: For crystallization of V2c-SVBP C58S in complex with the maTail peptide the components were mixed in a 1:3 molar ratio and incubated at room temperature for 24 h before setting up crystallization trials. The resulting V2c-SVBP S58C-maTail complex was crystallized in 1.4 M sodium/potassium phosphate, pH 8.2. PH range: 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 28792 / % possible obs: 99 % / Redundancy: 9.6 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.04 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2635 / CC1/2: 0.866 / Rpim(I) all: 0.196 / % possible all: 91.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6J4O Resolution: 2.1→38.045 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.09
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→38.045 Å
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Refine LS restraints |
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LS refinement shell |
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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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