+Open data
-Basic information
Entry | Database: PDB / ID: 6k7o | ||||||
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Title | Complex structure of LILRB4 and h128-3 antibody | ||||||
Components |
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Keywords | IMMUNE SYSTEM / LILRB4 / antibody / Immune therapy. | ||||||
Function / homology | Function and homology information transmembrane receptor protein tyrosine kinase inhibitor activity / negative regulation of cytotoxic T cell differentiation / negative regulation of IP-10 production / interleukin-10-mediated signaling pathway / negative regulation of T cell costimulation / tolerance induction / negative regulation of protein tyrosine kinase activity / inhibitory MHC class I receptor activity / Fc receptor mediated inhibitory signaling pathway / negative regulation of T cell cytokine production ...transmembrane receptor protein tyrosine kinase inhibitor activity / negative regulation of cytotoxic T cell differentiation / negative regulation of IP-10 production / interleukin-10-mediated signaling pathway / negative regulation of T cell costimulation / tolerance induction / negative regulation of protein tyrosine kinase activity / inhibitory MHC class I receptor activity / Fc receptor mediated inhibitory signaling pathway / negative regulation of T cell cytokine production / negative regulation of interleukin-5 production / positive regulation of CD8-positive, alpha-beta T cell differentiation / negative regulation of monocyte activation / positive regulation of T cell anergy / signaling receptor inhibitor activity / negative regulation of chemokine production / positive regulation of regulatory T cell differentiation / negative regulation of protein localization to nucleus / negative regulation of interleukin-1 beta production / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / negative regulation of MAPK cascade / negative regulation of interleukin-10 production / negative regulation of osteoclast differentiation / negative regulation of activated T cell proliferation / negative regulation of interleukin-6 production / apolipoprotein binding / fibronectin binding / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / negative regulation of cytokine production involved in inflammatory response / negative regulation of canonical NF-kappaB signal transduction / negative regulation of T cell proliferation / negative regulation of signaling receptor activity / negative regulation of miRNA transcription / receptor internalization / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / protein phosphatase binding / adaptive immune response / cell surface / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.004 Å | ||||||
Authors | Song, H. / Chai, Y. / Xu, X. / Gao, F.G. | ||||||
Citation | Journal: Cancer Immunol Res / Year: 2019 Title: Disrupting LILRB4/APOE Interaction by an Efficacious Humanized Antibody Reverses T-cell Suppression and Blocks AML Development. Authors: Gui, X. / Deng, M. / Song, H. / Chen, Y. / Xie, J. / Li, Z. / He, L. / Huang, F. / Xu, Y. / Anami, Y. / Yu, H. / Yu, C. / Li, L. / Yuan, Z. / Xu, X. / Wang, Q. / Chai, Y. / Huang, T. / Shi, ...Authors: Gui, X. / Deng, M. / Song, H. / Chen, Y. / Xie, J. / Li, Z. / He, L. / Huang, F. / Xu, Y. / Anami, Y. / Yu, H. / Yu, C. / Li, L. / Yuan, Z. / Xu, X. / Wang, Q. / Chai, Y. / Huang, T. / Shi, Y. / Tsuchikama, K. / Liao, X.C. / Xia, N. / Gao, G.F. / Zhang, N. / Zhang, C.C. / An, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k7o.cif.gz | 406.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k7o.ent.gz | 335.2 KB | Display | PDB format |
PDBx/mmJSON format | 6k7o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/6k7o ftp://data.pdbj.org/pub/pdb/validation_reports/k7/6k7o | HTTPS FTP |
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-Related structure data
Related structure data | 3p2tS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 10898.212 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LILRB4, ILT3, LIR5 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8NHJ6 #2: Antibody | Mass: 24208.961 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) #3: Antibody | Mass: 23758.234 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) |
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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: 3.95 Å3/Da / Density % sol: 68.88 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium dihydrogen phosphate, 0.1M Tris pH8.5, 50 % v/v MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.0401 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0401 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 72345 / % possible obs: 99.7 % / Redundancy: 5.1 % / Net I/σ(I): 15.971 |
Reflection shell | Resolution: 3→3.11 Å / Mean I/σ(I) obs: 2.595 / Num. unique obs: 7232 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3P2T Resolution: 3.004→44.214 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.004→44.214 Å
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Refine LS restraints |
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LS refinement shell |
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