+Open data
-Basic information
Entry | Database: PDB / ID: 6mhr | |||||||||
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Title | Structure of the human 4-1BB / Urelumab Fab complex | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Signaling / TNFRSF / 4-1BB / CD137 / therapeutic antibody / complex | |||||||||
Function / homology | Function and homology information TNFs bind their physiological receptors / regulation of immature T cell proliferation in thymus / signaling receptor activity / regulation of cell population proliferation / negative regulation of cell population proliferation / external side of plasma membrane / apoptotic process / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 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: Chin, S.M. / Kimberlin, C.R. / Roe-Zurz, Z. / Zhang, P. / Xu, A. / Liao-Chan, S. / Sen, D. / Nager, A.R. / Oakdale, N.S. / Brown, C. / Wang, F. / Yang, Y. / Lindquist, K. / Yeung, Y.A. / ...Authors: Chin, S.M. / Kimberlin, C.R. / Roe-Zurz, Z. / Zhang, P. / Xu, A. / Liao-Chan, S. / Sen, D. / Nager, A.R. / Oakdale, N.S. / 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 | 6mhr.cif.gz | 224.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mhr.ent.gz | 181.3 KB | Display | PDB format |
PDBx/mmJSON format | 6mhr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mhr_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6mhr_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6mhr_validation.xml.gz | 42.2 KB | Display | |
Data in CIF | 6mhr_validation.cif.gz | 58.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/6mhr ftp://data.pdbj.org/pub/pdb/validation_reports/mh/6mhr | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules FC
#3: Protein | Mass: 15670.648 Da / Num. of mol.: 2 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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-Antibody , 2 types, 4 molecules DAEB
#1: Antibody | Mass: 25393.252 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) #2: Antibody | Mass: 23519.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) |
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-Sugars , 2 types, 2 molecules
#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Polysaccharide | alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 20 molecules
#6: Chemical | ChemComp-GOL / | ||||
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#7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.94 Å3/Da / Density % sol: 75.11 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1M sodium malonate, pH 7.0, 0.4% v/v Jeffamine ED-2001 pH7.0, 0.1M HEPES pH7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1271 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 21, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.8→49.65 Å / Num. obs: 63589 / % possible obs: 100 % / Redundancy: 26.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.223 / Rpim(I) all: 0.044 / Rrim(I) all: 0.227 / Net I/σ(I): 15.8 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→49.649 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.69 / 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: 153.44 Å2 / Biso mean: 79.1608 Å2 / Biso min: 39.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→49.649 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %
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