+Open data
-Basic information
Entry | Database: PDB / ID: 6ux8 | ||||||
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Title | Structure of monobody 33 MLKL N-terminal domain complex | ||||||
Components |
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Keywords | TRANSFERASE / Protein interactions / cell death / RIPK3 / programmed necrosis / protein engineering | ||||||
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 | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Birkinshaw, R.W. / Petrie, E.J. / Murphy, J.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Identification of MLKL membrane translocation as a checkpoint in necroptotic cell death using Monobodies. Authors: Petrie, E.J. / Birkinshaw, R.W. / Koide, A. / Denbaum, E. / Hildebrand, J.M. / Garnish, S.E. / Davies, K.A. / Sandow, J.J. / Samson, A.L. / Gavin, X. / Fitzgibbon, C. / Young, S.N. / ...Authors: Petrie, E.J. / Birkinshaw, R.W. / Koide, A. / Denbaum, E. / Hildebrand, J.M. / Garnish, S.E. / Davies, K.A. / Sandow, J.J. / Samson, A.L. / Gavin, X. / Fitzgibbon, C. / Young, S.N. / Hennessy, P.J. / Smith, P.P.C. / Webb, A.I. / Czabotar, P.E. / Koide, S. / Murphy, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ux8.cif.gz | 112.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ux8.ent.gz | 84.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ux8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/6ux8 ftp://data.pdbj.org/pub/pdb/validation_reports/ux/6ux8 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18290.121 Da / Num. of mol.: 1 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 | ||||
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#2: Antibody | Mass: 10425.380 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Gene: Monobody / Production host: Escherichia coli (E. coli) | ||||
#3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% PEG-MME 550, 0.1 M MES pH 6.5, 0.01 M Zinc acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→68.04 Å / Num. obs: 8590 / % possible obs: 99.8 % / Redundancy: 5.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.081 / Rrim(I) all: 0.191 / Net I/σ(I): 7 / Num. measured all: 46234 / Scaling rejects: 1 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.506 / Num. measured all: 4761 / Num. unique obs: 937 / CC1/2: 0.477 / Rpim(I) all: 0.745 / Rrim(I) all: 1.688 / Net I/σ(I) obs: 1.2 / % possible all: 99.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6D0J, 4BTF Resolution: 2.5→44.76 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 181.93 Å2 / Biso mean: 65.1355 Å2 / Biso min: 31.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→44.76 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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