+Open data
-Basic information
Entry | Database: PDB / ID: 6mkz | |||||||||
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Title | Crystal structure of murine 4-1BB/4-1BBL complex | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / TNF / TNFR | |||||||||
Function / homology | Function and homology information TNFs bind their physiological receptors / tumor necrosis factor receptor superfamily binding / positive regulation of cytotoxic T cell differentiation / regulation of immature T cell proliferation in thymus / myeloid dendritic cell differentiation / tumor necrosis factor receptor binding / positive regulation of activated T cell proliferation / positive regulation of interleukin-12 production / cytokine activity / positive regulation of interleukin-6 production ...TNFs bind their physiological receptors / tumor necrosis factor receptor superfamily binding / positive regulation of cytotoxic T cell differentiation / regulation of immature T cell proliferation in thymus / myeloid dendritic cell differentiation / tumor necrosis factor receptor binding / positive regulation of activated T cell proliferation / positive regulation of interleukin-12 production / cytokine activity / positive regulation of interleukin-6 production / positive regulation of type II interferon production / signaling receptor activity / regulation of cell population proliferation / immune response / negative regulation of cell population proliferation / external side of plasma membrane / signaling receptor binding / apoptotic process / extracellular space / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | |||||||||
Authors | Bitra, A. / Zajonc, D.M. / Doukov, T. | |||||||||
Citation | Journal: J. Biol. Chem. / Year: 2019 Title: Crystal structure of the m4-1BB/4-1BBL complex reveals an unusual dimeric ligand that undergoes structural changes upon 4-1BB receptor binding. Authors: Bitra, A. / Doukov, T. / Destito, G. / Croft, M. / Zajonc, D.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mkz.cif.gz | 227.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mkz.ent.gz | 179.6 KB | Display | PDB format |
PDBx/mmJSON format | 6mkz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/6mkz ftp://data.pdbj.org/pub/pdb/validation_reports/mk/6mkz | HTTPS FTP |
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-Related structure data
Related structure data | 6mkbSC 5wi8S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 19258.646 Da / Num. of mol.: 2 / Fragment: residues 139-309 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfsf9, Cd137l, Cd157l, Ly63l / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41274 #2: Protein | Mass: 15147.186 Da / Num. of mol.: 2 / Fragment: residues 24-160 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfrsf9, Cd137, Ila, Ly63 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P20334 #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.9 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 4000, 0.2M ammonium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2018 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.624→76.859 Å / Num. obs: 25447 / % possible obs: 97.6 % / Redundancy: 13.7 % / Biso Wilson estimate: 76.59 Å2 / CC1/2: 0.96 / Net I/σ(I): 5.6 / Num. measured all: 349768 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WI8, 6MKB Resolution: 2.65→30.76 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.897 / SU R Cruickshank DPI: 0.384 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.417 / SU Rfree Blow DPI: 0.261 / SU Rfree Cruickshank DPI: 0.258
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Displacement parameters | Biso max: 218.79 Å2 / Biso mean: 85.39 Å2 / Biso min: 24.15 Å2
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Refine analyze | Luzzati coordinate error obs: 0.35 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.65→30.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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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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