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- PDB-4btf: Structure of MLKL -

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Basic information

Entry
Database: PDB / ID: 4btf
TitleStructure of MLKL
ComponentsMIXED LINEAGE KINASE DOMAIN-LIKE PROTEIN
KeywordsTRANSFERASE / PSEDUOKINASE / NECROPTOSIS
Function / homology
Function and homology information


RIPK1-mediated regulated necrosis / execution phase of necroptosis / Regulation of necroptotic cell death / necroptotic signaling pathway / TRP channels / protein homotrimerization / necroptotic process / cell junction / defense response to virus / cell surface receptor signaling pathway ...RIPK1-mediated regulated necrosis / execution phase of necroptosis / Regulation of necroptotic cell death / necroptotic signaling pathway / TRP channels / protein homotrimerization / necroptotic process / cell junction / defense response to virus / cell surface receptor signaling pathway / protein-containing complex binding / protein kinase binding / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Adaptor protein Cbl, N-terminal domain / Adaptor protein Cbl, N-terminal domain superfamily / Transcription Elongation Factor S-II; Chain A / 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. ...Adaptor protein Cbl, N-terminal domain / Adaptor protein Cbl, N-terminal domain superfamily / Transcription Elongation Factor S-II; Chain A / 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 / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Mixed lineage kinase domain-like protein
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.604 Å
AuthorsCzabotar, P.E. / Murphy, J.M.
CitationJournal: Immunity / Year: 2013
Title: The Pseudokinase Mlkl Mediates Necroptosis Via a Molecular Switch Mechanism
Authors: Murphy, J.M. / Czabotar, P.E. / Hildebrand, J.M. / Lucet, I.S. / Zhang, J.-G. / Alvarez-Diaz, S. / Lewis, R. / Lalaoui, N. / Metcalf, D. / Webb, A.I. / Young, S.N. / Varghese, L.N. / ...Authors: Murphy, J.M. / Czabotar, P.E. / Hildebrand, J.M. / Lucet, I.S. / Zhang, J.-G. / Alvarez-Diaz, S. / Lewis, R. / Lalaoui, N. / Metcalf, D. / Webb, A.I. / Young, S.N. / Varghese, L.N. / Tannahill, G.M. / Hatchell, E.C. / Majewski, I.J. / Okamoto, T. / Dobson, R.C.J. / Hilton, D.J. / Babon, J.J. / Nicola, N.A. / Strasser, A. / Silke, J. / Alexander, W.S.
History
DepositionJun 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Apr 24, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: MIXED LINEAGE KINASE DOMAIN-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0274
Polymers53,8571
Non-polymers1703
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.400, 78.300, 162.938
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 MIXED LINEAGE KINASE DOMAIN-LIKE PROTEIN / MLKL


Mass: 53856.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9D2Y4
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE MATCHES NCBI ENTRY NP_083281.1

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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: 2.51 Å3/Da / Density % sol: 51.08 % / Description: NONE
Crystal growDetails: 0.4M SODIUM FORMATE, 25% W/V PEG2000 MONOMETHYL ETHER, 50MM TRIS PH 7.5, 5MM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953696, 1.5498
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2010
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9536961
21.54981
ReflectionResolution: 2.6→50 Å / Num. obs: 16375 / % possible obs: 94.3 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 38.29 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.13
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.05 / % possible all: 82.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.604→41.033 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2555 811 4.9 %
Rwork0.2069 --
obs0.2093 16368 94.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.5 Å2
Refinement stepCycle: LAST / Resolution: 2.604→41.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3334 0 11 41 3386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083396
X-RAY DIFFRACTIONf_angle_d1.1044562
X-RAY DIFFRACTIONf_dihedral_angle_d16.7121328
X-RAY DIFFRACTIONf_chiral_restr0.075510
X-RAY DIFFRACTIONf_plane_restr0.004587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6037-2.76680.32451220.28532329X-RAY DIFFRACTION87
2.7668-2.98040.31711400.26122596X-RAY DIFFRACTION96
2.9804-3.28020.27281410.22312662X-RAY DIFFRACTION98
3.2802-3.75460.25171390.18912622X-RAY DIFFRACTION97
3.7546-4.72930.20951500.17052637X-RAY DIFFRACTION96
4.7293-41.03850.25391190.20782711X-RAY DIFFRACTION93
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)
12.92250.16320.7932.4011-0.56484.79710.20980.0308-0.110.04670.062-0.09391.20160.9094-0.27690.52580.1826-0.0360.51060.02730.29295.3454-9.0051-2.8981
21.0814-0.15620.06971.4076-0.33490.4524-0.03080.1566-0.0548-0.13180.05130.02260.0093-0.0382-0.0007-0.0366-0.01790.01350.3349-0.04070.086212.618216.066629.6037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 2 THROUGH 131 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 132 THROUGH 455 )

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