+Open data
-Basic information
Entry | Database: PDB / ID: 8yu9 | ||||||
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Title | Tubulin-RB3-TTL in complex with compound SI10 | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Inhibitor / tubulin / complex | ||||||
Function / homology | Function and homology information tubulin-tyrosine ligase / 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 / 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 / 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 / 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 / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / mitotic cell cycle / growth cone / microtubule / neuron projection / GTPase activity / GTP binding / Golgi apparatus / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) Rattus norvegicus (Norway rat) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Wu, C.Y. / Wang, Y.X. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: The crystal structure of tubulin-RB3-TTL in complex with compound AB10 Authors: Wu, C.Y. / Wang, Y.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8yu9.cif.gz | 873.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8yu9.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8yu9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8yu9_validation.pdf.gz | 959.8 KB | Display | wwPDB validaton report |
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Full document | 8yu9_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8yu9_validation.xml.gz | 85.7 KB | Display | |
Data in CIF | 8yu9_validation.cif.gz | 113.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/8yu9 ftp://data.pdbj.org/pub/pdb/validation_reports/yu/8yu9 | HTTPS FTP |
-Related structure data
Related structure data | 6d88S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 48966.324 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: 48391.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: TUBB2B / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8D0VN39 #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: 43825.914 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: A0A8V0Z8P0, tubulin-tyrosine ligase |
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-Non-polymers , 7 types, 14 molecules
#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | Mass: 346.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H11ClN4O2S / Feature type: SUBJECT OF INVESTIGATION #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-ACP / | |
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-Details
Has ligand of interest | Y |
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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: 2.96 Å3/Da / Density % sol: 58.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 6% PEG 4000, 5% Glycerol, 0.1 M MES, 30 mM CaCl2, 30 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→182.63 Å / Num. obs: 43659 / % possible obs: 89.8 % / Redundancy: 10.8 % / CC1/2: 0.558 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 3.25→3.42 Å / Num. unique obs: 6974 / CC1/2: 0.891 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6D88 Resolution: 3.25→87.33 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.25→87.33 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: 17.4224 Å / Origin y: -43.9064 Å / Origin z: -25.3901 Å
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Refinement TLS group | Selection details: all |