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- PDB-6d74: Direct Activation of the Executioner Domain of MLKL by a Select R... -

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Basic information

Entry
Database: PDB / ID: 6d74
TitleDirect Activation of the Executioner Domain of MLKL by a Select Repertoire of Inositol Phosphates
ComponentsMixed lineage kinase domain-like protein
KeywordsLIPID BINDING PROTEIN / Membrane
Function / homology
Function and homology information


execution phase of necroptosis / Microbial modulation of RIPK1-mediated regulated necrosis / necroptotic signaling pathway / TRP channels / RIPK1-mediated regulated necrosis / protein homotrimerization / necroptotic process / Regulation of necroptotic cell death / cell junction / defense response to virus ...execution phase of necroptosis / Microbial modulation of RIPK1-mediated regulated necrosis / necroptotic signaling pathway / TRP channels / RIPK1-mediated regulated necrosis / protein homotrimerization / necroptotic process / Regulation of necroptotic cell death / cell junction / defense response to virus / cell surface receptor signaling pathway / protein-containing complex binding / protein kinase binding / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Adaptor protein Cbl, N-terminal domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Mixed lineage kinase domain-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics / simulated annealing
AuthorsRoyappa, G.C. / McNamara, D.E. / Moldoveanu, T.
Citation
Journal: Cell Chem Biol / Year: 2019
Title: Direct Activation of Human MLKL by a Select Repertoire of Inositol Phosphate Metabolites.
Authors: McNamara, D.E. / Dovey, C.M. / Hale, A.T. / Quarato, G. / Grace, C.R. / Guibao, C.D. / Diep, J. / Nourse, A. / Cai, C.R. / Wu, H. / Kalathur, R.C. / Green, D.R. / York, J.D. / Carette, J.E. / Moldoveanu, T.
#1: Journal: Mol. Cell / Year: 2018
Title: MLKL Requires the Inositol Phosphate Code to Execute Necroptosis.
Authors: Dovey, C.M. / Diep, J. / Clarke, B.P. / Hale, A.T. / McNamara, D.E. / Guo, H. / Brown, N.W. / Cao, J.Y. / Grace, C.R. / Gough, P.J. / Bertin, J. / Dixon, S.J. / Fiedler, D. / Mocarski, E.S. ...Authors: Dovey, C.M. / Diep, J. / Clarke, B.P. / Hale, A.T. / McNamara, D.E. / Guo, H. / Brown, N.W. / Cao, J.Y. / Grace, C.R. / Gough, P.J. / Bertin, J. / Dixon, S.J. / Fiedler, D. / Mocarski, E.S. / Kaiser, W.J. / Moldoveanu, T. / York, J.D. / Carette, J.E.
History
DepositionApr 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mixed lineage kinase domain-like protein


Theoretical massNumber of molelcules
Total (without water)18,3181
Polymers18,3181
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9880 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 18318.129 Da / Num. of mol.: 1 / Fragment: residues 1-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLKL / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NB16

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic23D 1H-15N NOESY
131isotropic23D 1H-13C NOESY aliphatic
141isotropic23D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution / Contents: 500 uM [U-13C; U-15N] protein, 90% H2O/10% D2O / Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 500 uM / Component: protein / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 0 mM / Label: conditions_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
CARA1.9Keller and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.9Keller and Wuthrichpeak picking
TopSpin3.5Bruker Biospincollection
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
Refinement
MethodSoftware ordinal
torsion angle dynamics1
simulated annealing6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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