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- PDB-7jxu: Structure of monobody 32 human MLKL pseudokinase domain complex -

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Basic information

Entry
Database: PDB / ID: 7jxu
TitleStructure of monobody 32 human MLKL pseudokinase domain complex
Components
  • Mixed lineage kinase domain-like protein
  • Monobody 32
KeywordsTRANSFERASE / pseudokinase / monobody / complex / 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
Mixed lineage kinase domain-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsMeng, Y. / Garnish, S.E. / Koide, A. / Koide, S. / Czabotar, P.E. / Murphy, J.M.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1172929 Australia
National Health and Medical Research Council (NHMRC, Australia)1124735 Australia
CitationJournal: Nat Commun / Year: 2021
Title: Conformational interconversion of MLKL and disengagement from RIPK3 precede cell death by necroptosis.
Authors: Garnish, S.E. / Meng, Y. / Koide, A. / Sandow, J.J. / Denbaum, E. / Jacobsen, A.V. / Yeung, W. / Samson, A.L. / Horne, C.R. / Fitzgibbon, C. / Young, S.N. / Smith, P.P.C. / Webb, A.I. / ...Authors: Garnish, S.E. / Meng, Y. / Koide, A. / Sandow, J.J. / Denbaum, E. / Jacobsen, A.V. / Yeung, W. / Samson, A.L. / Horne, C.R. / Fitzgibbon, C. / Young, S.N. / Smith, P.P.C. / Webb, A.I. / Petrie, E.J. / Hildebrand, J.M. / Kannan, N. / Czabotar, P.E. / Koide, S. / Murphy, J.M.
History
DepositionAug 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: 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.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 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 protein
B: Mixed lineage kinase domain-like protein
D: Monobody 32
C: Monobody 32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5048
Polymers87,2564
Non-polymers2484
Water1,47782
1
A: Mixed lineage kinase domain-like protein
C: Monobody 32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7524
Polymers43,6282
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-3 kcal/mol
Surface area18070 Å2
MethodPISA
2
B: Mixed lineage kinase domain-like protein
D: Monobody 32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7524
Polymers43,6282
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-1 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.619, 94.619, 115.197
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 32736.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLKL / Plasmid: pFastBac Htb / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8NB16
#2: Antibody Monobody 32 /


Mass: 10891.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pPROEX / Production host: Escherichia coli BL21 (bacteria)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.958467 Å3/Da / Density % sol: 58.45024 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris chloride, pH 6.5, 20 % w/v PEG monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 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: Jun 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.44→49.2 Å / Num. obs: 37642 / % possible obs: 99.7 % / Redundancy: 7.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.041 / Rrim(I) all: 0.11 / Net I/σ(I): 9.5 / Num. measured all: 266899 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.44-2.546.71.4572780641340.5970.6041.578197.6
8.8-49.270.03657928320.9920.0150.03934.499.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M67, 5N7E

4m67

5n7e


Resolution: 2.44→42.31 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 1992 5.3 %
Rwork0.2018 35568 -
obs0.2039 37560 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.57 Å2 / Biso mean: 63.388 Å2 / Biso min: 30.69 Å2
Refinement stepCycle: final / Resolution: 2.44→42.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5966 0 16 82 6064
Biso mean--61.64 54.05 -
Num. residues----748
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.44-2.50.34031360.31082400253695
2.5-2.570.33751420.280825772719100
2.57-2.650.31351390.268125232662100
2.65-2.730.28321450.273925282673100
2.73-2.830.31171400.262425412681100
2.83-2.940.27951440.271725572701100
2.94-3.080.36761430.26225332676100
3.08-3.240.30031410.250225322673100
3.24-3.440.28031420.222425642706100
3.44-3.710.26491440.223725492693100
3.71-4.080.21941440.182325432687100
4.08-4.670.21741380.158725632701100
4.67-5.880.18811470.170825732720100
5.88-42.310.17211470.152425852732100

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