+Open data
-Basic information
Entry | Database: PDB / ID: 6nyh | ||||||
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Title | Structure of human RIPK1 kinase domain in complex with GNE684 | ||||||
Components | Receptor-interacting serine/threonine-protein kinase 1 | ||||||
Keywords | IMMUNE SYSTEM / RIP1 / kinase / RIP / RIP1K RIPK1 / Transferase-Transferase inhibitor complex | ||||||
Function / homology | Function and homology information regulation of ATP:ADP antiporter activity / ripoptosome assembly / positive regulation of interleukin-6-mediated signaling pathway / positive regulation of miRNA processing / ripoptosome assembly involved in necroptotic process / death domain binding / ripoptosome / Defective RIPK1-mediated regulated necrosis / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death ...regulation of ATP:ADP antiporter activity / ripoptosome assembly / positive regulation of interleukin-6-mediated signaling pathway / positive regulation of miRNA processing / ripoptosome assembly involved in necroptotic process / death domain binding / ripoptosome / Defective RIPK1-mediated regulated necrosis / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death / Microbial modulation of RIPK1-mediated regulated necrosis / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / programmed necrotic cell death / TNF signaling / Caspase activation via Death Receptors in the presence of ligand / T cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / positive regulation of macrophage differentiation / necroptotic signaling pathway / JUN kinase kinase kinase activity / peptidyl-serine autophosphorylation / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of necroptotic process / RIP-mediated NFkB activation via ZBP1 / death-inducing signaling complex / negative regulation of necroptotic process / positive regulation of tumor necrosis factor-mediated signaling pathway / death receptor binding / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of programmed cell death / TRP channels / positive regulation of programmed necrotic cell death / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / positive regulation of execution phase of apoptosis / necroptotic process / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / response to tumor necrosis factor / signaling adaptor activity / extrinsic apoptotic signaling pathway / negative regulation of canonical NF-kappaB signal transduction / tumor necrosis factor-mediated signaling pathway / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / Regulation of TNFR1 signaling / positive regulation of JNK cascade / protein catabolic process / Regulation of necroptotic cell death / cellular response to growth factor stimulus / cellular response to hydrogen peroxide / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of tumor necrosis factor production / positive regulation of reactive oxygen species metabolic process / positive regulation of neuron apoptotic process / Ovarian tumor domain proteases / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / response to oxidative stress / amyloid fibril formation / Potential therapeutics for SARS / protein autophosphorylation / receptor complex / non-specific serine/threonine protein kinase / endosome membrane / Ub-specific processing proteases / protein kinase activity / intracellular signal transduction / inflammatory response / positive regulation of protein phosphorylation / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / ATP binding / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Fong, R. / Lupardus, P.J. | ||||||
Citation | Journal: Cell Death Differ. / Year: 2020 Title: RIP1 inhibition blocks inflammatory diseases but not tumor growth or metastases. Authors: Patel, S. / Webster, J.D. / Varfolomeev, E. / Kwon, Y.C. / Cheng, J.H. / Zhang, J. / Dugger, D.L. / Wickliffe, K.E. / Maltzman, A. / Sujatha-Bhaskar, S. / Bir Kohli, P. / Ramaswamy, S. / ...Authors: Patel, S. / Webster, J.D. / Varfolomeev, E. / Kwon, Y.C. / Cheng, J.H. / Zhang, J. / Dugger, D.L. / Wickliffe, K.E. / Maltzman, A. / Sujatha-Bhaskar, S. / Bir Kohli, P. / Ramaswamy, S. / Deshmukh, G. / Liederer, B.M. / Fong, R. / Hamilton, G. / Lupardus, P. / Caplazi, P. / Lee, W.P. / van Lookeren Campagne, M. / Johnson, A. / McKenzie, B.S. / Junttila, M.R. / Newton, K. / Vucic, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nyh.cif.gz | 121.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nyh.ent.gz | 91.5 KB | Display | PDB format |
PDBx/mmJSON format | 6nyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nyh_validation.pdf.gz | 993.7 KB | Display | wwPDB validaton report |
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Full document | 6nyh_full_validation.pdf.gz | 999.3 KB | Display | |
Data in XML | 6nyh_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 6nyh_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/6nyh ftp://data.pdbj.org/pub/pdb/validation_reports/ny/6nyh | HTTPS FTP |
-Related structure data
Related structure data | 4ithS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33612.855 Da / Num. of mol.: 2 / Mutation: C34A, C127A, C233A, C240A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RIPK1, RIP, RIP1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q13546, non-specific serine/threonine protein kinase #2: Chemical | #3: Chemical | ChemComp-IOD / #4: Water | ChemComp-HOH / | |
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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: 2.12 Å3/Da / Density % sol: 42.07 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion Details: 0.1 M Bis Tris Propane buffer (pH 6.5), 0.2 M sodium iodide, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→48.52 Å / Num. obs: 32257 / % possible obs: 94.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 30.2 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.106 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.723 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ITH Resolution: 2.1→48.517 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.25
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→48.517 Å
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Refine LS restraints |
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LS refinement shell |
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