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- PDB-4m68: Crystal structure of the mouse MLKL kinase-like domain -

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Basic information

Entry
Database: PDB / ID: 4m68
TitleCrystal structure of the mouse MLKL kinase-like domain
ComponentsMixed lineage kinase domain-like protein
KeywordsSIGNALING PROTEIN / Kinase-like / substrate of RIP3 / RIP3
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 / 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 / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.696 Å
AuthorsXie, T. / Peng, W. / Yan, C. / Wu, J. / Shi, Y.
CitationJournal: Cell Rep / Year: 2013
Title: Structural Insights into RIP3-Mediated Necroptotic Signaling
Authors: Xie, T. / Peng, W. / Yan, C. / Wu, J. / Gong, X. / Shi, Y.
History
DepositionAug 9, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,3502
Polymers32,2581
Non-polymers921
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.970, 61.522, 60.074
Angle α, β, γ (deg.)90.00, 100.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 32258.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mlkl / Production host: Escherichia coli (E. coli) / References: UniProt: Q9D2Y4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE IS ISOFORM 2 OF Q9D2Y4 (MLKL_MOUSE).

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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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.3M potassium formate, 13% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Oct 5, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. all: 39964 / Num. obs: 39125 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 14.97 Å2
Reflection shellResolution: 1.6→1.66 Å / % possible all: 86.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M67

4m67


Resolution: 1.696→27.916 Å / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.8515 / SU ML: 0.18 / σ(F): 1.35 / Phase error: 21.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1687 5.07 %random
Rwork0.1935 ---
all0.1947 33452 --
obs0.1947 33258 99.42 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.824 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 96.14 Å2 / Biso mean: 27.4528 Å2 / Biso min: 6.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.6264 Å20 Å22.8347 Å2
2---2.9249 Å20 Å2
3---7.7064 Å2
Refinement stepCycle: LAST / Resolution: 1.696→27.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 6 290 2434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062226
X-RAY DIFFRACTIONf_angle_d1.0243008
X-RAY DIFFRACTIONf_chiral_restr0.063335
X-RAY DIFFRACTIONf_plane_restr0.009389
X-RAY DIFFRACTIONf_dihedral_angle_d16.174862
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6959-1.74580.27211570.24662473263094
1.7458-1.80220.26981520.23342588274099
1.8022-1.86660.24911240.210326562780100
1.8666-1.94130.21321250.204926312756100
1.9413-2.02960.18381290.198726442773100
2.0296-2.13660.21971550.201726302785100
2.1366-2.27040.21661340.195526432777100
2.2704-2.44560.23341370.202626502787100
2.4456-2.69150.22991490.201726372786100
2.6915-3.08050.20891390.200526532792100
3.0805-3.87950.19791640.173726472811100
3.8795-27.91940.20451220.174227192841100
Refinement TLS params.Method: refined / Origin x: -5.0801 Å / Origin y: 10.3438 Å / Origin z: -10.5902 Å
111213212223313233
T0.0284 Å20.0097 Å20.0002 Å2-0.0374 Å2-0.0047 Å2--0.0048 Å2
L2.0733 °2-0.3506 °20.0504 °2-1.6745 °2-0.1363 °2--0.887 °2
S0.0507 Å °0.2622 Å °0.0445 Å °-0.1703 Å °-0.0444 Å °-0.0757 Å °0.0223 Å °0.0813 Å °0.0053 Å °
Refinement TLS groupSelection details: ALL

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