+Open data
-Basic information
Entry | Database: PDB / ID: 5z4u | ||||||
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Title | Crystal Structure of T2R-TTL complex with 7a3 | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / TUBULIN / COMPLEX / INHIBITOR | ||||||
Function / homology | Function and homology information tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins ...tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / positive regulation of axon guidance / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / microtubule depolymerization / COPI-mediated anterograde transport / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / spindle microtubule / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / nervous system development / mitotic cell cycle / growth cone / microtubule / neuron projection / protein heterodimerization activity / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) Bos taurus (cattle) Rattus norvegicus (Norway rat) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å | ||||||
Authors | Lai, Q. / Wang, Y. / Yang, J. / Yao, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of T2R-TTL complex with 7a3 Authors: Lai, Q. / Wang, Y. / Yang, J. / Yao, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z4u.cif.gz | 445.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z4u.ent.gz | 355.4 KB | Display | PDB format |
PDBx/mmJSON format | 5z4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z4u_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 5z4u_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 5z4u_validation.xml.gz | 71.7 KB | Display | |
Data in CIF | 5z4u_validation.cif.gz | 97 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z4/5z4u ftp://data.pdbj.org/pub/pdb/validation_reports/z4/5z4u | HTTPS FTP |
-Related structure data
Related structure data | 4o2bS S: Starting model for refinement |
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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 , 4 types, 6 molecules ACBDEF
#1: Protein | Mass: 50041.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: TUBA1B / Production host: Escherichia coli (E. coli) / References: UniProt: Q2XVP4 #2: Protein | Mass: 49937.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: TUBB2B / Production host: Escherichia coli (E. coli) / References: UniProt: Q6B856 #3: Protein | | Mass: 16844.162 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043 #4: Protein | | Mass: 44378.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL / Production host: Escherichia coli (E. coli) / References: UniProt: E1BQ43 |
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-Non-polymers , 7 types, 16 molecules
#5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | #8: Chemical | ChemComp-GDP / | #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-ACP / | |
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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: 3.08 Å3/Da / Density % sol: 60.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 6% poly(ethylene glycol) 4000, 8% glycerol, 0.1 M Mes, 30 mM CaCl2, 30 mM MgCl2 (pH 6.7) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 3.18→120 Å / Num. obs: 50942 / % possible obs: 98.7 % / Redundancy: 6.9 % / Net I/σ(I): 12 |
Reflection shell | Resolution: 3.2→3.26 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4O2B Resolution: 3.18→119.44 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.889 / SU B: 21.972 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R Free: 0.484 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.931 Å2
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Refinement step | Cycle: 1 / Resolution: 3.18→119.44 Å
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