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- PDB-4ith: Crystal structure of RIP1 kinase in complex with necrostatin-1 analog -

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Basic information

Entry
Database: PDB / ID: 4ith
TitleCrystal structure of RIP1 kinase in complex with necrostatin-1 analog
ComponentsReceptor-interacting serine/threonine-protein kinase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / alpha/beta / RIP1 kinase / necroptosis / necrostatins / KINASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


ripoptosome assembly / positive regulation of miRNA processing / positive regulation of interleukin-6-mediated signaling pathway / ripoptosome assembly involved in necroptotic process / death domain binding / peptidyl-serine autophosphorylation / ripoptosome / Defective RIPK1-mediated regulated necrosis / Microbial modulation of RIPK1-mediated regulated necrosis / TRIF-mediated programmed cell death ...ripoptosome assembly / positive regulation of miRNA processing / positive regulation of interleukin-6-mediated signaling pathway / ripoptosome assembly involved in necroptotic process / death domain binding / peptidyl-serine autophosphorylation / ripoptosome / Defective RIPK1-mediated regulated necrosis / Microbial modulation of RIPK1-mediated regulated necrosis / TRIF-mediated programmed cell death / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / TLR3-mediated TICAM1-dependent programmed cell death / TNF signaling / programmed necrotic cell death / Caspase activation via Death Receptors in the presence of ligand / SARS-CoV-1-mediated effects on programmed cell death / positive regulation of macrophage differentiation / JUN kinase kinase kinase activity / T cell apoptotic process / necroptotic signaling pathway / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / death-inducing signaling complex / RIP-mediated NFkB activation via ZBP1 / positive regulation of necroptotic process / negative regulation of necroptotic process / positive regulation of tumor necrosis factor-mediated signaling pathway / death receptor binding / positive regulation of programmed cell death / positive regulation of programmed necrotic cell death / positive regulation of extrinsic apoptotic signaling pathway / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / TRP channels / necroptotic process / response to tumor necrosis factor / positive regulation of execution phase of apoptosis / canonical NF-kappaB signal transduction / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / extrinsic apoptotic signaling pathway / signaling adaptor activity / negative regulation of canonical NF-kappaB signal transduction / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / Regulation of TNFR1 signaling / protein catabolic process / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / cellular response to growth factor stimulus / Regulation of necroptotic cell death / cellular response to hydrogen peroxide / positive regulation of protein phosphorylation / positive regulation of reactive oxygen species metabolic process / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / cellular response to tumor necrosis factor / Ovarian tumor domain proteases / positive regulation of neuron apoptotic process / protein autophosphorylation / response to oxidative stress / amyloid fibril formation / Potential therapeutics for SARS / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / receptor complex / protein kinase activity / endosome membrane / Ub-specific processing proteases / intracellular signal transduction / positive regulation of apoptotic process / inflammatory response / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / ubiquitin protein ligase binding / positive regulation of gene expression / negative regulation of apoptotic process / protein-containing complex binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / ATP binding / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
RIP1, Death domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / : / Death-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 ...RIP1, Death domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / : / Death-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Chem-RCM / Receptor-interacting serine/threonine-protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsXie, T. / Peng, W. / Liu, Y. / Yan, C. / Shi, Y.
CitationJournal: Structure / Year: 2013
Title: Structural Basis of RIP1 Inhibition by Necrostatins.
Authors: Xie, T. / Peng, W. / Liu, Y. / Yan, C. / Maki, J. / Degterev, A. / Yuan, J. / Shi, Y.
History
DepositionJan 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor-interacting serine/threonine-protein kinase 1
B: Receptor-interacting serine/threonine-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,80816
Polymers66,9372
Non-polymers1,87014
Water2,378132
1
A: Receptor-interacting serine/threonine-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4048
Polymers33,4691
Non-polymers9357
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Receptor-interacting serine/threonine-protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4048
Polymers33,4691
Non-polymers9357
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.128, 93.605, 129.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Receptor-interacting serine/threonine-protein kinase 1 / Cell death protein RIP / Receptor-interacting protein 1 / RIP-1 / Serine/threonine-protein kinase RIP


Mass: 33468.730 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
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-RCM / (5R)-5-[(7-chloro-1H-indol-3-yl)methyl]-3-methylimidazolidine-2,4-dione


Mass: 277.706 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12ClN3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.25 M NH4I, 20% polyethylene glycol (PEG) 3350, 0.03 M glycyl-glycyl-glycine, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 11, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→40 Å / Num. all: 27731 / Num. obs: 27706 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.25→2.33 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3C4C

3c4c


Resolution: 2.25→37.888 Å / SU ML: 0.34 / σ(F): 0 / Phase error: 26.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 1395 5.04 %Random
Rwork0.2208 ---
obs0.2222 27706 99.6 %-
all-27731 --
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.716 Å2 / ksol: 0.322 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.1891 Å20 Å2-0 Å2
2--8.807 Å2-0 Å2
3----5.9427 Å2
Refinement stepCycle: LAST / Resolution: 2.25→37.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4038 0 50 132 4220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114173
X-RAY DIFFRACTIONf_angle_d1.3375644
X-RAY DIFFRACTIONf_dihedral_angle_d17.1251538
X-RAY DIFFRACTIONf_chiral_restr0.191641
X-RAY DIFFRACTIONf_plane_restr0.006708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.33180.34211400.29012547X-RAY DIFFRACTION99
2.3318-2.42520.28731260.25792583X-RAY DIFFRACTION99
2.4252-2.53550.28251240.252607X-RAY DIFFRACTION100
2.5355-2.66920.33871530.2552580X-RAY DIFFRACTION100
2.6692-2.83640.30151330.24742614X-RAY DIFFRACTION100
2.8364-3.05530.22881160.23982638X-RAY DIFFRACTION100
3.0553-3.36260.24961430.23082653X-RAY DIFFRACTION100
3.3626-3.84870.21771580.20942623X-RAY DIFFRACTION100
3.8487-4.84740.21381490.17942685X-RAY DIFFRACTION100
4.8474-37.89310.24051530.2142781X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.44160.2733-0.33745.4977-0.2331.4064-0.27760.16280.5928-0.6714-0.08830.5017-0.9544-0.80180.14840.70880.1715-0.16980.2092-0.04970.4135-27.627913.017411.3756
22.4002-1.5871-0.45874.32331.33122.5319-0.0979-0.2009-0.32330.1150.3606-0.33950.53950.6383-0.23590.36520.0962-0.08590.411-0.00410.3614-4.1704-69.770528.1698
32.5735-0.37750.67873.06691.6654.50720.06240.0048-0.1385-0.03380.0773-0.14220.16520.1777-0.07810.16060.0222-0.01540.1264-0.00770.1873-20.6207-12.280910.6497
41.45720.1256-0.29772.8673-1.28592.70120.1166-0.17540.10490.002-0.0759-0.1414-0.23390.2835-0.05110.1981-0.03410.00390.2934-0.05510.1566-11.1518-45.502122.3624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 10:93
2X-RAY DIFFRACTION2CHAIN B AND RESID 10:93
3X-RAY DIFFRACTION3CHAIN A AND RESID 112:293
4X-RAY DIFFRACTION4CHAIN B AND RESID 112:293

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