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Yorodumi- PDB-1lk3: ENGINEERED HUMAN INTERLEUKIN-10 MONOMER COMPLEXED TO 9D7 FAB FRAGMENT -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lk3 | ||||||
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Title | ENGINEERED HUMAN INTERLEUKIN-10 MONOMER COMPLEXED TO 9D7 FAB FRAGMENT | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ANTIGEN-ANTIBODY COMPLEX | ||||||
Function / homology | Function and homology information Classical antibody-mediated complement activation / FCGR activation / Regulation of Complement cascade / negative regulation of chronic inflammatory response to antigenic stimulus / interleukin-10 receptor binding / regulation of response to wounding / negative regulation of cytokine activity / Role of phospholipids in phagocytosis / negative regulation of interleukin-18 production / negative regulation of myeloid dendritic cell activation ...Classical antibody-mediated complement activation / FCGR activation / Regulation of Complement cascade / negative regulation of chronic inflammatory response to antigenic stimulus / interleukin-10 receptor binding / regulation of response to wounding / negative regulation of cytokine activity / Role of phospholipids in phagocytosis / negative regulation of interleukin-18 production / negative regulation of myeloid dendritic cell activation / Initial triggering of complement / negative regulation of interferon-alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / response to carbon monoxide / positive regulation of B cell apoptotic process / positive regulation of plasma cell differentiation / response to inactivity / Regulation of actin dynamics for phagocytic cup formation / chronic inflammatory response to antigenic stimulus / cytoplasmic sequestering of NF-kappaB / negative regulation of membrane protein ectodomain proteolysis / regulation of isotype switching / negative regulation of heterotypic cell-cell adhesion / negative regulation of cytokine production involved in immune response / negative regulation of interleukin-1 production / positive regulation of B cell activation / negative regulation of MHC class II biosynthetic process / negative regulation of interleukin-8 production / branching involved in labyrinthine layer morphogenesis / negative regulation of nitric oxide biosynthetic process / phagocytosis, recognition / negative regulation of interleukin-12 production / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / type 2 immune response / endothelial cell apoptotic process / positive regulation of macrophage activation / positive regulation of MHC class II biosynthetic process / leukocyte chemotaxis / positive regulation of signaling receptor activity / positive regulation of heterotypic cell-cell adhesion / CD163 mediating an anti-inflammatory response / negative regulation of cytokine production / phagocytosis, engulfment / cellular response to hepatocyte growth factor stimulus / regulation of synapse organization / immunoglobulin complex, circulating / positive regulation of sprouting angiogenesis / B cell proliferation / immunoglobulin receptor binding / defense response to protozoan / negative regulation of B cell proliferation / negative regulation of vascular associated smooth muscle cell proliferation / Interleukin-10 signaling / negative regulation of interleukin-6 production / hemopoiesis / negative regulation of type II interferon production / positive regulation of immunoglobulin production / negative regulation of tumor necrosis factor production / negative regulation of mitotic cell cycle / positive regulation of cell cycle / complement activation, classical pathway / response to glucocorticoid / negative regulation of T cell proliferation / positive regulation of vascular associated smooth muscle cell proliferation / antigen binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of endothelial cell proliferation / FCGR3A-mediated IL10 synthesis / negative regulation of autophagy / B cell differentiation / response to activity / cytokine activity / cellular response to estradiol stimulus / liver regeneration / positive regulation of cytokine production / B cell receptor signaling pathway / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / response to insulin / response to molecule of bacterial origin / negative regulation of inflammatory response / positive regulation of miRNA transcription / positive regulation of DNA-binding transcription factor activity / regulation of gene expression / Interleukin-4 and Interleukin-13 signaling / cellular response to lipopolysaccharide / protein dimerization activity / defense response to bacterium / response to xenobiotic stimulus / negative regulation of cell population proliferation / external side of plasma membrane / innate immune response / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Josephson, K. / Jones, B.C. / Walter, L.J. / DiGiacomo, R. / Indelicato, S.R. / Walter, M.R. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Noncompetitive antibody neutralization of IL-10 revealed by protein engineering and x-ray crystallography. Authors: Josephson, K. / Jones, B.C. / Walter, L.J. / DiGiacomo, R. / Indelicato, S.R. / Walter, M.R. #1: Journal: J.Biol.Chem. / Year: 2000 Title: Design and Analysis of an Engineered Human Interleukin-10 Monomer Authors: Josephson, K. / DiGiacomo, R. / Indelicato, S.R. / Iyo, A.H. / Nagabhushan, T.L. / Parker, M.H. / Walter, M.R. / Ayo, A.H. | ||||||
History |
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Remark 999 | SEQUENCE USING BLAST NO APPROPRIATE SEQUENCE DATABASE MATCH WAS FOUND FOR 9D7 LIGHT CHAIN, CHAINS ...SEQUENCE USING BLAST NO APPROPRIATE SEQUENCE DATABASE MATCH WAS FOUND FOR 9D7 LIGHT CHAIN, CHAINS L,M AND 9D7 HEAVY CHAIN, CHAINS H,I. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lk3.cif.gz | 251.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lk3.ent.gz | 207.9 KB | Display | PDB format |
PDBx/mmJSON format | 1lk3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/1lk3 ftp://data.pdbj.org/pub/pdb/validation_reports/lk/1lk3 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar 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
#1: Protein | Mass: 18520.324 Da / Num. of mol.: 2 / Fragment: Residues 26-175 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL10 / Plasmid: pET32lic / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P22301 #2: Antibody | Mass: 22794.438 Da / Num. of mol.: 2 / Fragment: Fab fragment, Residues 1-210 / Source method: isolated from a natural source / Details: Hybridoma / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P01835*PLUS #3: Antibody | Mass: 23529.443 Da / Num. of mol.: 2 / Fragment: Fab fragment, Residues 1-219 / Source method: isolated from a natural source / Details: Hybridoma / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P20759*PLUS #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: 2.67 Å3/Da / Density % sol: 54.01 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: peg 4000, sodium citrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 1999 |
Radiation | Monochromator: Si(311) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→50 Å / Num. all: 96708 / Num. obs: 96708 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 3.7 % / Biso Wilson estimate: 23.11 Å2 / Rsym value: 0.049 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.91→1.95 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.34 / % possible all: 72.6 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 357669 / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS % possible obs: 72.6 % / Rmerge(I) obs: 0.34 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.91→50 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 50 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |