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- PDB-7jw7: Structure of monobody 27 human MLKL pseudokinase domain complex -

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Basic information

Entry
Database: PDB / ID: 7jw7
TitleStructure of monobody 27 human MLKL pseudokinase domain complex
Components
  • Mixed lineage kinase domain-like protein
  • Monobody 27
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 / RIPK1-mediated regulated necrosis / TRP channels / 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 / RIPK1-mediated regulated necrosis / TRP channels / protein homotrimerization / necroptotic process / Regulation of necroptotic cell death / cell junction / defense response to virus / cell surface receptor signaling pathway / protein kinase binding / protein-containing complex binding / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Mixed lineage kinase domain-like N-terminal domain / Adaptor protein Cbl, N-terminal domain superfamily / : / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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: 2.63 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 25, 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: Monobody 27


Theoretical massNumber of molelcules
Total (without water)43,4032
Polymers43,4032
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-8 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.805, 64.805, 226.763
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 32736.750 Da / Num. of mol.: 1
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 27


Mass: 10666.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pPROEX / Production host: Escherichia coli BL21 (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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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: 3.170734 Å3/Da / Density % sol: 61.23182 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M magnesium chloride, 20% w/v PEG 3350

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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: 2.63→45.35 Å / Num. obs: 17332 / % possible obs: 99.8 % / Redundancy: 9.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.038 / Rrim(I) all: 0.12 / Net I/σ(I): 11.1 / Num. measured all: 171651 / Scaling rejects: 1
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
2.63-2.7410.21.7142097620480.9160.5541.8031.399
9.1-45.358.20.0341084980.9990.0110.03238.799.1

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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, 6UX8

4m67

6ux8


Resolution: 2.63→45.06 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 37.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2815 1721 10.04 %
Rwork0.2242 15426 -
obs0.23 17147 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.92 Å2 / Biso mean: 81.3182 Å2 / Biso min: 38.74 Å2
Refinement stepCycle: final / Resolution: 2.63→45.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2772 0 0 10 2782
Biso mean---68.95 -
Num. residues----345
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.63-2.70.50541430.41571251139498
2.7-2.790.40761390.3661223136299
2.79-2.890.47381380.35221232137098
2.89-3.010.35651460.33011273141999
3.01-3.140.43981350.28761264139999
3.15-3.310.30211390.26241265140498
3.31-3.520.33191440.23791282142699
3.52-3.790.26631440.23771277142199
3.79-4.170.30431410.198512831424100
4.17-4.770.20791470.17713211468100
4.77-6.010.23861490.191213291478100
6.01-45.060.22761560.191214261582100

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