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- PDB-6bwk: Crystal structure of the human MLKL pseudokinase domain T357E/S35... -

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Basic information

Entry
Database: PDB / ID: 6bwk
TitleCrystal structure of the human MLKL pseudokinase domain T357E/S358E mutant
ComponentsMixed lineage kinase domain-like protein
KeywordsTRANSFERASE / Pseudokinase / Necroptosis
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 / cytoplasm / cytosol
Similarity search - Function
Adaptor protein Cbl, N-terminal domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily ...Adaptor protein Cbl, N-terminal domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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
Mixed lineage kinase domain-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsCowan, A.D. / Czabotar, P.E. / Murphy, J.M.
Funding support Australia, 7items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1124735 Australia
National Health and Medical Research Council (NHMRC, Australia)1057905 Australia
National Health and Medical Research Council (NHMRC, Australia)9000220 Australia
National Health and Medical Research Council (NHMRC, Australia)1105754 Australia
National Health and Medical Research Council (NHMRC, Australia)1079700 Australia
National Health and Medical Research Council (NHMRC, Australia)1058190 Australia
National Health and Medical Research Council (NHMRC, Australia)1117089 Australia
CitationJournal: Nat Commun / Year: 2018
Title: Conformational switching of the pseudokinase domain promotes human MLKL tetramerization and cell death by necroptosis.
Authors: Petrie, E.J. / Sandow, J.J. / Jacobsen, A.V. / Smith, B.J. / Griffin, M.D.W. / Lucet, I.S. / Dai, W. / Young, S.N. / Tanzer, M.C. / Wardak, A. / Liang, L.Y. / Cowan, A.D. / Hildebrand, J.M. ...Authors: Petrie, E.J. / Sandow, J.J. / Jacobsen, A.V. / Smith, B.J. / Griffin, M.D.W. / Lucet, I.S. / Dai, W. / Young, S.N. / Tanzer, M.C. / Wardak, A. / Liang, L.Y. / Cowan, A.D. / Hildebrand, J.M. / Kersten, W.J.A. / Lessene, G. / Silke, J. / Czabotar, P.E. / Webb, A.I. / Murphy, J.M.
History
DepositionDec 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 9, 2020Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mixed lineage kinase domain-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1755
Polymers32,8071
Non-polymers3684
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-4 kcal/mol
Surface area13210 Å2
Unit cell
Length a, b, c (Å)72.114, 74.723, 127.601
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 32806.797 Da / Num. of mol.: 1 / Fragment: UNP Residues 190-471 / Mutation: T357E S358E
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
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 5% w/v polyethylene glycol 8000, 20% v/v polyethylene glycol 300, 0.1M Tris chloride pH 8.5, 10% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 8516 / % possible obs: 97.3 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rrim(I) all: 0.235 / Net I/σ(I): 8.28
Reflection shellResolution: 2.79→2.97 Å / Redundancy: 5.2 % / Num. unique obs: 1168 / CC1/2: 0.141 / Rrim(I) all: 4.54 / % possible all: 84.2

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSJun 1, 2017data reduction
XDSJun 1, 2017data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MWI

4mwi


Resolution: 2.79→40.257 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.76
RfactorNum. reflection% reflectionSelection details
Rfree0.2972 400 4.87 %R-free flags copied from 4MWI reflection file
Rwork0.2549 ---
obs0.257 8211 92.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.79→40.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 24 4 1988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072017
X-RAY DIFFRACTIONf_angle_d0.7692737
X-RAY DIFFRACTIONf_dihedral_angle_d14.7711212
X-RAY DIFFRACTIONf_chiral_restr0.047323
X-RAY DIFFRACTIONf_plane_restr0.005347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7897-3.19320.45561060.43872138X-RAY DIFFRACTION77
3.1932-4.02250.32381450.29982780X-RAY DIFFRACTION99
4.0225-40.26070.26251490.20982893X-RAY DIFFRACTION100
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)
13.7628-0.6058-0.23262.45070.47032.81450.15930.48450.8616-0.4328-0.07010.1033-1.0774-0.2648-0.0911.01110.0972-0.00350.54610.12940.725411.428154.373160.7605
22.1721.4357-1.08212.25221.62534.7442-0.12870.34850.7265-0.1198-0.13290.7587-0.8255-0.04870.25970.82420.0757-0.13360.6240.15720.73257.455947.562456.3797
36.72711.1832-1.48113.16880.56965.52870.02610.91550.2143-0.57120.00810.1834-0.1345-0.0283-0.0470.67180.0722-0.06790.54270.03520.388623.568237.440641.1079
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 192 through 240 )
2X-RAY DIFFRACTION2chain 'A' and (resid 241 through 290 )
3X-RAY DIFFRACTION3chain 'A' and (resid 291 through 470 )

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