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- PDB-7mon: Structure of human RIPK3-MLKL complex -

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Basic information

Entry
Database: PDB / ID: 7mon
TitleStructure of human RIPK3-MLKL complex
Components
  • Mixed lineage kinase domain-like protein
  • Receptor-interacting serine/threonine-protein kinase 3
KeywordsTRANSFERASE / 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 / T cell homeostasis / protein homotrimerization / 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 / 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 / cytosol / cytoplasm
Similarity search - Function
RHIM domain / RIP homotypic interaction motif / Adaptor protein Cbl, N-terminal domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...RHIM domain / RIP homotypic interaction motif / Adaptor protein Cbl, N-terminal domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-ZL1 / Mixed lineage kinase domain-like protein / Receptor-interacting serine/threonine-protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.23 Å
AuthorsMeng, Y. / Davies, K.A. / Czabotar, P.E. / Murphy, J.M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1172929 Australia
CitationJournal: 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
DepositionMay 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mixed lineage kinase domain-like protein
B: Receptor-interacting serine/threonine-protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8064
Polymers67,8022
Non-polymers1,0052
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-14 kcal/mol
Surface area25290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.495, 82.839, 104.842
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mixed lineage kinase domain-like protein / hMLKL


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
#2: Protein Receptor-interacting serine/threonine-protein kinase 3 / RIP-like protein kinase 3 / Receptor-interacting protein 3 / RIP-3


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 ChemComp-ZL1 / N-[4-({2-[(cyclopropanecarbonyl)amino]pyridin-4-yl}oxy)-3-fluorophenyl]-1-(4-fluorophenyl)-2-oxo-1,2-dihydropyridine-3-carboxamide


Mass: 502.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H20F2N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.45 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.23-2.36.61.3461601224290.6160.5551.4591.194.9
8.91-45.785.90.03629935110.9990.0150.03932.998

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.89 Å41.42 Å
Translation3.89 Å41.42 Å

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JXU, 4M69

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
RfactorNum. reflection% reflection
Rfree0.2601 2000 7.15 %
Rwork0.2089 25990 -
obs0.2125 27990 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.84 Å2 / Biso mean: 43.6036 Å2 / Biso min: 19.96 Å2
Refinement stepCycle: final / Resolution: 2.23→41.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4365 0 74 105 4544
Biso mean--50.35 39.49 -
Num. residues----553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024531
X-RAY DIFFRACTIONf_angle_d0.5196134
X-RAY DIFFRACTIONf_chiral_restr0.04682
X-RAY DIFFRACTIONf_plane_restr0.004783
X-RAY DIFFRACTIONf_dihedral_angle_d21.4411702
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.23-2.280.351320.29571715184793
2.28-2.340.30421410.287318281969100
2.34-2.410.35251400.267118331973100
2.41-2.490.33281420.256318351977100
2.49-2.580.3061420.248118541996100
2.58-2.680.2911430.241918431986100
2.68-2.810.32121410.231618371978100
2.81-2.950.27031420.228918431985100
2.95-3.140.26371430.221718561999100
3.14-3.380.291450.215518812026100
3.38-3.720.27031430.189118772020100
3.72-4.260.19331450.168818782023100
4.26-5.360.2331470.1719142061100
5.37-41.420.22381540.2011996215099

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