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Yorodumi- PDB-6j8f: Crystal structure of SVBP-VASH1 with peptide mimic the C-terminal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j8f | ||||||||||||
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Title | Crystal structure of SVBP-VASH1 with peptide mimic the C-terminal of alpha-tubulin | ||||||||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN/HYDROLASE / protease / complex / PEPTIDE BINDING PROTEIN / Structural Genomics / PSI-2 / Protein Structure Initiative / Structural Genomics Consortium / SGC / PEPTIDE BINDING PROTEIN-HYDROLASE complex | ||||||||||||
Function / homology | Function and homology information regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Post-chaperonin tubulin folding pathway / axonemal microtubule / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / regulation of cellular senescence / Carboxyterminal post-translational modifications of tubulin / negative regulation of lymphangiogenesis ...regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Post-chaperonin tubulin folding pathway / axonemal microtubule / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / regulation of cellular senescence / Carboxyterminal post-translational modifications of tubulin / negative regulation of lymphangiogenesis / organelle transport along microtubule / peptidase activator activity / glial cell differentiation / forebrain morphogenesis / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / neuron projection arborization / cytoskeleton-dependent intracellular transport / cerebellar cortex morphogenesis / Formation of tubulin folding intermediates by CCT/TriC / dentate gyrus development / Gap junction assembly / COPI-independent Golgi-to-ER retrograde traffic / pyramidal neuron differentiation / Prefoldin mediated transfer of substrate to CCT/TriC / Kinesins / Hedgehog 'off' state / Assembly and cell surface presentation of NMDA receptors / centrosome cycle / motor behavior / negative regulation of endothelial cell migration / COPI-dependent Golgi-to-ER retrograde traffic / labyrinthine layer blood vessel development / response to L-glutamate / smoothened signaling pathway / regulation of synapse organization / axon development / startle response / negative regulation of endothelial cell proliferation / locomotory exploration behavior / Recycling pathway of L1 / microtubule polymerization / microtubule-based process / negative regulation of blood vessel endothelial cell migration / protein secretion / RHO GTPases activate IQGAPs / response to tumor necrosis factor / regulation of angiogenesis / response to mechanical stimulus / COPI-mediated anterograde transport / metallocarboxypeptidase activity / Activation of AMPK downstream of NMDARs / condensed chromosome / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / homeostasis of number of cells within a tissue / negative regulation of protein ubiquitination / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / cellular response to calcium ion / AURKA Activation by TPX2 / negative regulation of angiogenesis / adult locomotory behavior / Translocation of SLC2A4 (GLUT4) to the plasma membrane / intracellular protein transport / RHO GTPases Activate Formins / neuron migration / synapse organization / visual learning / neuromuscular junction / PKR-mediated signaling / recycling endosome / cerebral cortex development / structural constituent of cytoskeleton / memory / microtubule cytoskeleton organization / response to wounding / Aggrephagy / HCMV Early Events / cytoplasmic ribonucleoprotein granule / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / apical part of cell / mitotic cell cycle / actin binding / gene expression / microtubule binding / angiogenesis / neuron apoptotic process / microtubule / cytoskeleton Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.283 Å | ||||||||||||
Authors | Liao, S. / Gao, J. / Xu, C. / Structural Genomics Consortium (SGC) | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Cell Res. / Year: 2019 Title: Molecular basis of vasohibins-mediated detyrosination and its impact on spindle function and mitosis. Authors: Liao, S. / Rajendraprasad, G. / Wang, N. / Eibes, S. / Gao, J. / Yu, H. / Wu, G. / Tu, X. / Huang, H. / Barisic, M. / Xu, C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j8f.cif.gz | 120.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j8f.ent.gz | 92.7 KB | Display | PDB format |
PDBx/mmJSON format | 6j8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j8f_validation.pdf.gz | 445 KB | Display | wwPDB validaton report |
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Full document | 6j8f_full_validation.pdf.gz | 447.9 KB | Display | |
Data in XML | 6j8f_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 6j8f_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/6j8f ftp://data.pdbj.org/pub/pdb/validation_reports/j8/6j8f | HTTPS FTP |
-Related structure data
Related structure data | 6j7bC 6j8nC 6j91C 6j9hC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 5410.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SVBP, CCDC23 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8N300 |
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#2: Protein | Mass: 27668.096 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VASH1, KIAA1036, VASH / Production host: Escherichia coli (E. coli) / References: UniProt: Q7L8A9, tubulinyl-Tyr carboxypeptidase |
#3: Protein/peptide | Mass: 914.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q71U36*PLUS |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.85 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1M Na citrate tribasic dihydrate pH 5.0, 18% PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→54.19 Å / Num. obs: 16147 / % possible obs: 99.9 % / Redundancy: 12.5 % / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.28→2.41 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2322 / CC1/2: 0.726 / Rpim(I) all: 0.491 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: low resolution SeMet structure Resolution: 2.283→54.188 Å / SU ML: 0.25 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 27.74
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.283→54.188 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 26.5379 Å / Origin y: 19.938 Å / Origin z: 10.6746 Å
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Refinement TLS group | Selection details: all |