+Open data
-Basic information
Entry | Database: PDB / ID: 7mon | ||||||
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Title | Structure of human RIPK3-MLKL complex | ||||||
Components |
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Keywords | TRANSFERASE / pseudokinase / kinase / complex / necroptosis | ||||||
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 / non-canonical NF-kappaB signal transduction / T cell homeostasis / protein homotrimerization / 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 / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of reactive oxygen species metabolic process / cell junction / 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 / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex binding / protein kinase binding / signal transduction / protein-containing complex / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.23 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: 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 | 7mon.cif.gz | 130.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mon.ent.gz | 96.9 KB | Display | PDB format |
PDBx/mmJSON format | 7mon.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mon_validation.pdf.gz | 899.6 KB | Display | wwPDB validaton report |
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Full document | 7mon_full_validation.pdf.gz | 904.3 KB | Display | |
Data in XML | 7mon_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 7mon_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/7mon ftp://data.pdbj.org/pub/pdb/validation_reports/mo/7mon | HTTPS FTP |
-Related structure data
Related structure data | 7mx3C 4m69S 7jxuS 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
#1: Protein | Mass: 32736.750 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: Protein | Mass: 35064.777 Da / Num. of mol.: 1 / 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 | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.45 % |
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Crystal grow | Temperature: 281.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2 M ammonium acetate 30%w/v PEG 4000 0.1 M trisodium citrate-citric acid pH 5.5 |
-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: 0.9537 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 11, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.23→45.78 Å / Num. obs: 28056 / % possible obs: 99.4 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.06 / Rrim(I) all: 0.156 / Net I/σ(I): 8.3 / Num. measured all: 186701 / Scaling rejects: 17 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7JXU, 4M69 Resolution: 2.23→41.42 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.54 / 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: 127.84 Å2 / Biso mean: 43.6036 Å2 / Biso min: 19.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.23→41.42 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: 14
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