+Open data
-Basic information
Entry | Database: PDB / ID: 8eq6 | ||||||
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Title | PD1 signaling receptor bound to FAB Complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN/Immune System / Immune signaling receptor FAB complex / SIGNALING PROTEIN / SIGNALING PROTEIN-Immune System complex | ||||||
Function / homology | Function and homology information negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / negative regulation of immune response / B cell apoptotic process / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / regulation of immune response ...negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / negative regulation of immune response / B cell apoptotic process / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / regulation of immune response / PD-1 signaling / signaling receptor activity / Potential therapeutics for SARS / adaptive immune response / external side of plasma membrane / apoptotic process / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Bjorkelid, C. / Paluch, C. / Robertson, N.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Immunity / Year: 2024 Title: Antibody agonists trigger immune receptor signaling through local exclusion of receptor-type protein tyrosine phosphatases. Authors: Lippert, A.H. / Paluch, C. / Gaglioni, M. / Vuong, M.T. / McColl, J. / Jenkins, E. / Fellermeyer, M. / Clarke, J. / Sharma, S. / Moreira da Silva, S. / Akkaya, B. / Anzilotti, C. / Morgan, S. ...Authors: Lippert, A.H. / Paluch, C. / Gaglioni, M. / Vuong, M.T. / McColl, J. / Jenkins, E. / Fellermeyer, M. / Clarke, J. / Sharma, S. / Moreira da Silva, S. / Akkaya, B. / Anzilotti, C. / Morgan, S.H. / Jessup, C.F. / Korbel, M. / Gileadi, U. / Leitner, J. / Knox, R. / Chirifu, M. / Huo, J. / Yu, S. / Ashman, N. / Lui, Y. / Wilkinson, I. / Attfield, K.E. / Fugger, L. / Robertson, N.J. / Lynch, C.J. / Murray, L. / Steinberger, P. / Santos, A.M. / Lee, S.F. / Cornall, R.J. / Klenerman, D. / Davis, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8eq6.cif.gz | 204.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8eq6.ent.gz | 158.4 KB | Display | PDB format |
PDBx/mmJSON format | 8eq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8eq6_validation.pdf.gz | 444.7 KB | Display | wwPDB validaton report |
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Full document | 8eq6_full_validation.pdf.gz | 449.1 KB | Display | |
Data in XML | 8eq6_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 8eq6_validation.cif.gz | 30 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/8eq6 ftp://data.pdbj.org/pub/pdb/validation_reports/eq/8eq6 | HTTPS FTP |
-Related structure data
Related structure data | 6k0yS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14365.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Production host: Expression vector pcDNA-inf (others) / References: UniProt: Q15116 |
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#2: Antibody | Mass: 23442.916 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Expression vector pcDNA-inf (others) |
#3: Antibody | Mass: 24493.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Expression vector pcDNA-inf (others) |
#4: 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: 2.06 Å3/Da / Density % sol: 40.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 20.5% PEG 3350, 0.4M MgCl2, 0.1M Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 17, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→49.62 Å / Num. obs: 60066 / % possible obs: 98.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 15.86 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.066 / Rrim(I) all: 0.169 / Net I/av σ(I): 5.6 / Net I/σ(I): 4.86 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 4.1 % / Rmerge(I) obs: 2.329 / Mean I/σ(I) obs: 0.2 / Num. unique obs: 10635 / CC1/2: 0.338 / Rpim(I) all: 1.246 / Rrim(I) all: 2.657 / % possible all: 86.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6k0y Resolution: 1.65→49.616 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.196 / SU B: 5.284 / SU ML: 0.15 / Average fsc free: 0.919 / Average fsc work: 0.933 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.119 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.019 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→49.616 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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