+Open data
-Basic information
Entry | Database: PDB / ID: 7mx3 | ||||||
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Title | Crystal structure of human RIPK3 complexed with GSK'843 | ||||||
Components | Receptor-interacting serine/threonine-protein kinase 3 | ||||||
Keywords | TRANSFERASE/INHIBITOR / kinase / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / execution phase of necroptosis / regulation of T cell mediated cytotoxicity / regulation of adaptive immune response / regulation of activated T cell proliferation / positive regulation of phosphatase activity / regulation of type II interferon production / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death ...regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / execution phase of necroptosis / regulation of T cell mediated cytotoxicity / regulation of adaptive immune response / regulation of activated T cell proliferation / positive regulation of phosphatase activity / regulation of type II interferon production / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death / Microbial modulation of RIPK1-mediated regulated necrosis / programmed necrotic cell death / SARS-CoV-1-mediated effects on programmed cell death / necroptotic signaling pathway / positive regulation of necroptotic process / RIP-mediated NFkB activation via ZBP1 / TRP channels / RIPK1-mediated regulated necrosis / activation of protein kinase activity / T cell homeostasis / non-canonical NF-kappaB signal transduction / necroptotic process / lymph node development / positive regulation of intrinsic apoptotic signaling pathway / spleen development / reactive oxygen species metabolic process / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / thymus development / apoptotic signaling pathway / protein modification process / Regulation of necroptotic cell death / cellular response to hydrogen peroxide / positive regulation of reactive oxygen species metabolic process / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of NF-kappaB transcription factor activity / T cell differentiation in thymus / regulation of apoptotic process / defense response to virus / amyloid fibril formation / protein autophosphorylation / transcription coactivator activity / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex binding / signal transduction / protein-containing complex / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 Å | ||||||
Authors | Davies, K.A. / Czabotar, P.E. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Human RIPK3 maintains MLKL in an inactive conformation prior to cell death by necroptosis. Authors: Meng, Y. / Davies, K.A. / Fitzgibbon, C. / Young, S.N. / Garnish, S.E. / Horne, C.R. / Luo, C. / Garnier, J.M. / Liang, L.Y. / Cowan, A.D. / Samson, A.L. / Lessene, G. / Sandow, J.J. / ...Authors: Meng, Y. / Davies, K.A. / Fitzgibbon, C. / Young, S.N. / Garnish, S.E. / Horne, C.R. / Luo, C. / Garnier, J.M. / Liang, L.Y. / Cowan, A.D. / Samson, A.L. / Lessene, G. / Sandow, J.J. / 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 | 7mx3.cif.gz | 229 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mx3.ent.gz | 183.8 KB | Display | PDB format |
PDBx/mmJSON format | 7mx3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/7mx3 ftp://data.pdbj.org/pub/pdb/validation_reports/mx/7mx3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 35090.000 Da / Num. of mol.: 4 / Mutation: C3S, C110A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RIPK3, RIP3 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9Y572, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-ZOV / #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.47 Å3/Da / Density % sol: 50.26 % |
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Crystal grow | Temperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M magnesium chloride, 25% (w/v) polyethylene glycol 3350, 0.1 M Tris pH 8.5 |
-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: 0.95373 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 3.229→80.759 Å / Num. obs: 10790 / % possible obs: 90.7 % / Redundancy: 6.3 % / CC1/2: 0.979 / Rmerge(I) obs: 0.259 / Rpim(I) all: 0.113 / Rrim(I) all: 0.283 / Net I/σ(I): 3.4 |
Reflection shell | Resolution: 3.229→3.697 Å / Rmerge(I) obs: 1.031 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 540 / CC1/2: 0.451 / Rpim(I) all: 0.484 / Rrim(I) all: 1.142 / % possible all: 56.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: hRIPK3 from hRIPK3:hMLKL complex structure Resolution: 3.23→74.12 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.92 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 154.95 Å2 / Biso mean: 67.3477 Å2 / Biso min: 22.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.23→74.12 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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