+Open data
-Basic information
Entry | Database: PDB / ID: 6mgp | |||||||||
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Title | Structure of human 4-1BB / 4-1BBL complex | |||||||||
Components | (Tumor necrosis factor ...) x 2 | |||||||||
Keywords | IMMUNE SYSTEM / Signaling / TNFRSF / TNFSF / 4-1BB / CD137 / 4-1BBL / CD137L / complex | |||||||||
Function / homology | Function and homology information tumor necrosis factor receptor superfamily binding / positive regulation of cytotoxic T cell differentiation / TNFs bind their physiological receptors / regulation of immature T cell proliferation in thymus / tumor necrosis factor receptor binding / regulation of T cell proliferation / positive regulation of activated T cell proliferation / cytokine activity / cell-cell signaling / signaling receptor activity ...tumor necrosis factor receptor superfamily binding / positive regulation of cytotoxic T cell differentiation / TNFs bind their physiological receptors / regulation of immature T cell proliferation in thymus / tumor necrosis factor receptor binding / regulation of T cell proliferation / positive regulation of activated T cell proliferation / cytokine activity / cell-cell signaling / signaling receptor activity / regulation of cell population proliferation / regulation of apoptotic process / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | |||||||||
Authors | Kimberlin, C.R. / Chin, S.M. / Roe-Zurz, Z. / Xu, A. / Yang, Y. | |||||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Structure of the 4-1BB/4-1BBL complex and distinct binding and functional properties of utomilumab and urelumab Authors: Kimberlin, C.R. / Chin, S.M. / Roe-Zurz, Z. / Zhang, P. / Xu, A. / Liao-Chan, S. / Debasish, S. / Nager, A.R. / Schirle Oakdale, N. / Brown, C. / Wang, F. / Yang, Y. / Lindquist, K. / Yeung, ...Authors: Kimberlin, C.R. / Chin, S.M. / Roe-Zurz, Z. / Zhang, P. / Xu, A. / Liao-Chan, S. / Debasish, S. / Nager, A.R. / Schirle Oakdale, N. / Brown, C. / Wang, F. / Yang, Y. / Lindquist, K. / Yeung, Y.A. / Salek-Ardakani, S. / Chaparro-Riggers, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mgp.cif.gz | 349.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mgp.ent.gz | 285.1 KB | Display | PDB format |
PDBx/mmJSON format | 6mgp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mgp_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6mgp_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6mgp_validation.xml.gz | 33.9 KB | Display | |
Data in CIF | 6mgp_validation.cif.gz | 45.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/6mgp ftp://data.pdbj.org/pub/pdb/validation_reports/mg/6mgp | HTTPS FTP |
-Related structure data
Related structure data | 2x29S S: Starting model for refinement |
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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
-Tumor necrosis factor ... , 2 types, 6 molecules ABCXYZ
#1: Protein | Mass: 21937.758 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNFSF9 / Plasmid: pFastBac / Cell line (production host): HighFive / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P41273 #2: Protein | Mass: 15670.648 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF9, CD137, ILA / Plasmid: pFastBac / Cell line (production host): HighFive / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q07011 |
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-Sugars , 1 types, 3 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 3 types, 97 molecules
#4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-GOL / #6: 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: 2.98 Å3/Da / Density % sol: 58.71 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 7 Details: 2.5M sodium acetate pH 7.0 plus 0.1% w/v Ovalbumin, 0.0005% w/v Pepsin, 0.0005% w/v Proteinase K, 0.0005% w/v Trypsin, 0.002 M HEPES sodium pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→48.91 Å / Num. obs: 75083 / % possible obs: 99.6 % / Redundancy: 27.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.205 / Rpim(I) all: 0.04 / Rrim(I) all: 0.209 / Net I/σ(I): 17.1 / Num. measured all: 2039905 |
Reflection shell | Resolution: 2.13→2.17 Å / Redundancy: 27.7 % / Rmerge(I) obs: 10.329 / Num. unique obs: 4362 / CC1/2: 0.287 / Rpim(I) all: 1.977 / Rrim(I) all: 10.518 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2x29 Resolution: 2.13→48.907 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 165.95 Å2 / Biso mean: 70.9781 Å2 / Biso min: 34.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.13→48.907 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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