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- PDB-6zz1: Crystal structure of MLKL executioner domain in complex with a co... -

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Basic information

Entry
Database: PDB / ID: 6zz1
TitleCrystal structure of MLKL executioner domain in complex with a covalent inhibitor
ComponentsMixed lineage kinase domain-like protein
KeywordsLIPID BINDING PROTEIN / 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 / 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
Chem-QOK / Mixed lineage kinase domain-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsFiegen, D. / Bauer, M. / Nar, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Locking mixed-lineage kinase domain-like protein in its auto-inhibited state prevents necroptosis.
Authors: Rubbelke, M. / Fiegen, D. / Bauer, M. / Binder, F. / Hamilton, J. / King, J. / Thamm, S. / Nar, H. / Zeeb, M.
History
DepositionAug 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: 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
B: Mixed lineage kinase domain-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8214
Polymers35,2852
Non-polymers5372
Water2,774154
1
A: Mixed lineage kinase domain-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9112
Polymers17,6421
Non-polymers2681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mixed lineage kinase domain-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9112
Polymers17,6421
Non-polymers2681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.709, 56.709, 90.501
Angle α, β, γ (deg.)90, 90, 90
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 17642.326 Da / Num. of mol.: 2
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-QOK / 7-(2-methoxyethoxymethyl)-1,3-dimethyl-purine-2,6-dione


Mass: 268.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 32 % Polyethylene glycol monomethyl ether 2,000, 0.15 M Potassium bromide, 0.1 M TRIS, pH 9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99994 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99994 Å / Relative weight: 1
ReflectionResolution: 1.64→19.705 Å / Num. obs: 28984 / % possible obs: 82.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.029 / Rsym value: 0.029 / Net I/σ(I): 24.6
Reflection shellResolution: 1.64→1.746 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1449 / Rsym value: 0.797 / % possible all: 24.3

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
autoPROCdata reduction
XDSJan 31, 202data reduction
autoPROC1.1.7data scaling
Aimlessdata scaling
DIMPLEphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4btf

4btf


Resolution: 1.64→20.05 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.125 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.126 / SU Rfree Blow DPI: 0.118 / SU Rfree Cruickshank DPI: 0.119
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 1501 -RANDOM
Rwork0.1966 ---
obs0.1983 28985 82.8 %-
Displacement parametersBiso mean: 52.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.1109 Å20 Å20 Å2
2---0.1109 Å20 Å2
3---0.2219 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.64→20.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 38 154 2496
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012415HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.93235HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d931SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes449HARMONIC5
X-RAY DIFFRACTIONt_it2373HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion298SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2141SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion16.8
LS refinement shellResolution: 1.64→1.7 Å
RfactorNum. reflection% reflection
Rfree0.1848 36 -
Rwork0.2184 --
obs0.2162 580 15.54 %

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