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- PDB-6vc0: Crystal structure of the horse MLKL pseudokinase domain -

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Basic information

Entry
Database: PDB / ID: 6vc0
TitleCrystal structure of the horse MLKL pseudokinase domain
ComponentsMixed lineage kinase domain like pseudokinase
KeywordsTRANSFERASE / Cell death / necroptosis / pseudokinase
Function / homology
Function and homology information


: / execution phase of necroptosis / necroptotic signaling pathway / JUN kinase kinase kinase activity / protein homotrimerization / necroptotic process / defense response to virus / cell surface receptor signaling pathway / protein kinase activity / protein-containing complex binding ...: / execution phase of necroptosis / necroptotic signaling pathway / JUN kinase kinase kinase activity / protein homotrimerization / necroptotic process / defense response to virus / cell surface receptor signaling pathway / protein kinase activity / protein-containing complex binding / protein kinase binding / ATP binding / nucleus / plasma membrane / cytoplasm
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 pseudokinase
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.746 Å
AuthorsDavies, K.A. / Czabotar, P.E.
Funding support1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)
CitationJournal: Nat Commun / Year: 2020
Title: Distinct pseudokinase domain conformations underlie divergent activation mechanisms among vertebrate MLKL orthologues.
Authors: Davies, K.A. / Fitzgibbon, C. / Young, S.N. / Garnish, S.E. / Yeung, W. / Coursier, D. / Birkinshaw, R.W. / Sandow, J.J. / Lehmann, W.I.L. / Liang, L.Y. / Lucet, I.S. / Chalmers, J.D. / ...Authors: Davies, K.A. / Fitzgibbon, C. / Young, S.N. / Garnish, S.E. / Yeung, W. / Coursier, D. / Birkinshaw, R.W. / Sandow, J.J. / Lehmann, W.I.L. / Liang, L.Y. / Lucet, I.S. / Chalmers, J.D. / Patrick, W.M. / Kannan, N. / Petrie, E.J. / Czabotar, P.E. / Murphy, J.M.
History
DepositionDec 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Mixed lineage kinase domain like pseudokinase
B: Mixed lineage kinase domain like pseudokinase
C: Mixed lineage kinase domain like pseudokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1955
Polymers100,0113
Non-polymers1842
Water86548
1
A: Mixed lineage kinase domain like pseudokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4292
Polymers33,3371
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mixed lineage kinase domain like pseudokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4292
Polymers33,3371
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mixed lineage kinase domain like pseudokinase


Theoretical massNumber of molelcules
Total (without water)33,3371
Polymers33,3371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.532, 124.775, 81.053
Angle α, β, γ (deg.)90.000, 112.750, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Mixed lineage kinase domain like pseudokinase


Mass: 33337.098 Da / Num. of mol.: 3 / Fragment: pseudokinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: MLKL / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: F6S337
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.82 Å3/Da / Density % sol: 67.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2 M ammonium sulphate, 0.1 M sodium HEPES pH 7.5

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Data collection

DiffractionMean temperature: 293.15 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: Apr 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.74→43.953 Å / Num. obs: 37172 / % possible obs: 98.5 % / Redundancy: 6.912 % / Biso Wilson estimate: 53.53 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.189 / Rrim(I) all: 0.204 / Χ2: 0.972 / Net I/σ(I): 8.93 / Num. measured all: 256927
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.74-2.96.3921.4031.1135819607256040.5061.52692.3
2.9-3.17.3040.8662.1541611571056970.7890.93299.8
3.1-3.357.0720.4844.0837312528552760.9180.52499.8
3.35-3.676.7970.2687.2133155489348780.9710.29199.7
3.67-4.16.560.17311.2128909442144070.9850.18899.7
4.1-4.737.10.12416.1627797392839150.9940.13499.7
4.73-5.777.3680.1216.7624454332833190.9940.12999.7
5.77-8.116.8450.10317.5517757260125940.9940.11299.7
8.11-43.9536.8240.05728.9410113150214820.9980.06298.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4mwi

4mwi


Resolution: 2.746→43.953 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2384 2000 5.43 %
Rwork0.1709 34832 -
obs0.1747 36832 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 197.65 Å2 / Biso mean: 59.352 Å2 / Biso min: 21.94 Å2
Refinement stepCycle: final / Resolution: 2.746→43.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6585 0 12 48 6645
Biso mean--65.59 45.13 -
Num. residues----812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146729
X-RAY DIFFRACTIONf_angle_d1.2799060
X-RAY DIFFRACTIONf_chiral_restr0.0591004
X-RAY DIFFRACTIONf_plane_restr0.0081146
X-RAY DIFFRACTIONf_dihedral_angle_d18.1994114
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.746-2.81440.37661210.3158211284
2.8144-2.89050.35581430.2834249799
2.8905-2.97550.33571450.24482513100
2.9755-3.07150.30481420.21772485100
3.0715-3.18130.30481460.21882529100
3.1813-3.30860.29811430.20522516100
3.3086-3.45910.27431450.17482515100
3.4591-3.64140.23461430.1642484100
3.6414-3.86940.21531450.14732534100
3.8694-4.1680.23381440.13312512100
4.168-4.5870.16781440.11932506100
4.587-5.24980.20851450.13882537100
5.2498-6.61060.20921460.17412528100
6.6106-43.9530.21021480.1723256499
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)
14.1929-1.51970.0194.52060.37512.20240.2544-0.1483-0.5790.357-0.54220.93350.1638-0.27090.20630.351-0.1030.01460.60250.0560.4776-27.4002-47.350549.6676
23.101-0.0621-0.36262.6821-0.26881.47860.2096-0.3616-0.07850.4149-0.35810.2911-0.2259-0.36670.0810.3725-0.05550.11460.46530.02040.3069-25.3231-43.319148.6501
31.58640.72860.79672.02210.26291.49760.2403-0.1968-0.0861-0.00570.02240.27690.31-0.1763-0.1130.3819-0.017-0.02050.36990.03140.3914-29.2108-52.008441.7447
43.35120.60661.06292.5776-0.42962.37420.2149-0.33590.05520.3856-0.1866-0.0081-0.0177-0.01-0.00140.2756-0.03640.01370.32630.01460.2689-28.2703-35.514430.9492
52.61220.22340.41881.8809-0.00831.8085-0.14130.12110.2396-0.16010.02680.51950.0351-0.02360.08110.3424-0.0079-0.04010.308-0.00660.3868-41.952-33.709220.6425
62.256-0.021-0.31683.5170.08461.9696-0.0710.66370.2679-0.3989-0.0405-0.1589-0.10130.54530.15450.42610.0249-0.01230.57560.06890.3301-29.0414-33.644813.2126
72.96810.65480.15282.3437-0.49723.39210.3245-0.22070.43030.2093-0.13340.0524-0.44940.2625-0.11410.3565-0.05570.06170.3795-0.06880.4028-65.9424-50.798927.4858
81.71240.85320.45642.141-0.13751.1761-0.0873-0.07780.48920.41120.22230.13860.14650.042-0.12450.2763-0.0644-0.03180.47870.04680.482-51.1322-51.596625.7766
91.5906-0.60311.01852.2095-0.69060.6090.1585-0.1190.10220.0548-0.0945-0.0154-0.11660.0001-0.07210.3045-0.03930.03870.2967-0.02730.3031-59.6786-65.134532.753
103.52752.0752-0.96841.6861-0.53761.12180.3044-0.47330.03210.2742-0.4028-0.2092-0.19770.19260.12440.4084-0.1073-0.03120.41820.06470.3797-46.9964-67.417746.5881
112.39670.0538-0.85171.9978-0.24633.76310.1399-0.0956-0.9519-0.023-0.007-0.07460.53380.0993-0.25350.46940.0235-0.07750.36340.05950.5646-48.6629-81.647340.6174
122.7305-1.130.91251.9453-0.64434.13820.12720.3793-0.3941-0.37440.09140.01760.37580.1502-0.15080.3938-0.0319-0.01410.3027-0.03590.3619-64.6605-75.927311.3068
132.25930.2941.37011.88110.74053.48870.07880.0286-0.0381-0.0920.11020.01040.24730.1205-0.10410.22960.0006-0.00050.2405-0.01280.2529-81.2211-70.735320.6593
142.05040.5516-0.29011.2862-0.51613.18050.1522-0.05480.12690.04990.15710.2227-0.0944-0.4157-0.22020.2855-0.00950.0420.37930.06420.3253-95.342-66.054816.4559
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 189 through 211 )A189 - 211
2X-RAY DIFFRACTION2chain 'A' and (resid 212 through 229 )A212 - 229
3X-RAY DIFFRACTION3chain 'A' and (resid 230 through 281 )A230 - 281
4X-RAY DIFFRACTION4chain 'A' and (resid 282 through 370 )A282 - 370
5X-RAY DIFFRACTION5chain 'A' and (resid 371 through 435 )A371 - 435
6X-RAY DIFFRACTION6chain 'A' and (resid 436 through 467 )A436 - 467
7X-RAY DIFFRACTION7chain 'B' and (resid 189 through 229 )B189 - 229
8X-RAY DIFFRACTION8chain 'B' and (resid 230 through 253 )B230 - 253
9X-RAY DIFFRACTION9chain 'B' and (resid 254 through 345 )B254 - 345
10X-RAY DIFFRACTION10chain 'B' and (resid 346 through 435 )B346 - 435
11X-RAY DIFFRACTION11chain 'B' and (resid 436 through 468 )B436 - 468
12X-RAY DIFFRACTION12chain 'C' and (resid 189 through 281 )C189 - 281
13X-RAY DIFFRACTION13chain 'C' and (resid 282 through 370 )C282 - 370
14X-RAY DIFFRACTION14chain 'C' and (resid 371 through 471 )C371 - 471

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