+Open data
-Basic information
Entry | Database: PDB / ID: 7cnm | ||||||
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Title | YDX in complex with tubulin | ||||||
Components |
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Keywords | CELL CYCLE / YDX / tubulin / protein-drug complex | ||||||
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 / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / microtubule depolymerization / 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 / microtubule cytoskeleton / neuron projection development / mitotic cell cycle / growth cone / microtubule / neuron projection / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Gallus gallus (chicken) Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å | ||||||
Authors | Wang, Y.X. / Wu, C.Y. | ||||||
Citation | Journal: Febs Lett. / Year: 2021 Title: The high-resolution X-ray structure of vinca-domain inhibitors of microtubules provides a rational approach for drug design. Authors: Chengyong, W. / Jinghong, X. / Yanyan, W. / Qing-Jie, X. / Lingling, M. / Yuyan, L. / Hai, C. / Qian, L. / Quan, Z. / Bo, S. / Yuxi, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cnm.cif.gz | 456.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cnm.ent.gz | 364.5 KB | Display | PDB format |
PDBx/mmJSON format | 7cnm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cnm_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 7cnm_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 7cnm_validation.xml.gz | 76.5 KB | Display | |
Data in CIF | 7cnm_validation.cif.gz | 105 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/7cnm ftp://data.pdbj.org/pub/pdb/validation_reports/cn/7cnm | HTTPS FTP |
-Related structure data
Related structure data | 7cnnC 7cnoC 4i55S S: Starting model for refinement C: citing same article (ref.) |
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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: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4 #2: Protein | Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AGU7 #3: Protein | | Mass: 16844.162 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63042 #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 , 8 types, 309 molecules
#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-ACP / | #12: Water | ChemComp-HOH / | |
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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: 2.9 Å3/Da / Density % sol: 57.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: 6% PEG, 5% glycerol, 0.1 M MES, 30 mM CaCl2, 30 mM MgCl2, pH 6.7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.44→119.16 Å / Num. obs: 113201 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.032 / Rrim(I) all: 0.082 / Χ2: 0.927 / Net I/σ(I): 6.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4I55 Resolution: 2.44→119.16 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / SU B: 8.252 / SU ML: 0.182 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.365 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||
Displacement parameters | Biso max: 155.71 Å2 / Biso mean: 43.221 Å2 / Biso min: 12 Å2
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Refinement step | Cycle: final / Resolution: 2.44→119.16 Å
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LS refinement shell | Resolution: 2.44→2.503 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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