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Yorodumi- PDB-8slz: Crystal structure of phosphorylated (T357/S358) human MLKL pseudo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8slz | ||||||
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Title | Crystal structure of phosphorylated (T357/S358) human MLKL pseudokinase domain | ||||||
Components | Mixed lineage kinase domain-like protein | ||||||
Keywords | TRANSFERASE / pseudokinase / phosphorylation | ||||||
Function / homology | Function and homology information execution phase of necroptosis / Microbial modulation of RIPK1-mediated regulated necrosis / necroptotic signaling pathway / TRP channels / RIPK1-mediated regulated necrosis / protein homotrimerization / necroptotic process / Regulation of necroptotic cell death / cell junction / defense response to virus ...execution phase of necroptosis / Microbial modulation of RIPK1-mediated regulated necrosis / necroptotic signaling pathway / TRP channels / RIPK1-mediated regulated necrosis / protein homotrimerization / necroptotic process / Regulation of necroptotic cell death / cell junction / defense response to virus / cell surface receptor signaling pathway / protein-containing complex binding / protein kinase binding / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Meng, Y. / Davies, K.A. / Czabotar, P.E. / Murphy, J.M. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Phosphorylation-dependent pseudokinase domain dimerization drives full-length MLKL oligomerization. Authors: Meng, Y. / Garnish, S.E. / Davies, K.A. / Black, K.A. / Leis, A.P. / Horne, C.R. / Hildebrand, J.M. / Hoblos, H. / Fitzgibbon, C. / Young, S.N. / Dite, T. / Dagley, L.F. / Venkat, A. / ...Authors: Meng, Y. / Garnish, S.E. / Davies, K.A. / Black, K.A. / Leis, A.P. / Horne, C.R. / Hildebrand, J.M. / Hoblos, H. / Fitzgibbon, C. / Young, S.N. / Dite, T. / Dagley, L.F. / Venkat, A. / Kannan, N. / Koide, A. / Koide, S. / Glukhova, A. / Czabotar, P.E. / Murphy, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8slz.cif.gz | 68 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8slz.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 8slz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sl/8slz ftp://data.pdbj.org/pub/pdb/validation_reports/sl/8slz | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32896.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MLKL / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8NB16 |
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#2: 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: 2.57 Å3/Da / Density % sol: 52.07 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 20%w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953732 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47.72 Å / Num. obs: 15077 / % possible obs: 98.09 % / Redundancy: 6.7 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0711 / Rpim(I) all: 0.02981 / Rrim(I) all: 0.07727 / Χ2: 0.51 / Net I/σ(I): 16.21 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.9642 / Num. unique obs: 1427 / CC1/2: 0.748 / Rpim(I) all: 0.3922 / Rrim(I) all: 1.007 / Χ2: 0.37 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→40.02 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→40.02 Å
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Refine LS restraints |
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LS refinement shell |
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