+Open data
-Basic information
Entry | Database: PDB / ID: 3qwr | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of IL-23 in complex with an adnectin | |||||||||
Components |
| |||||||||
Keywords | PROTEIN BINDING/CYTOKINE / FOUR-HELIX BUNDLE CYTOKINE / IG DOMAIN / GLYCOPROTEIN / IMMUNOGLOBULIN DOMAIN / SECRETED / ANTIVIRAL DEFENSE / IMMUNE RESPONSE / INFLAMMATORY RESPONSE / INNATE IMMUNITY / TISSUE REMODELING / ADNECTIN / ENGINEERED BINDING PROTEIN / ANTIBODY MIMIC / PROTEIN BINDING-CYTOKINE complex | |||||||||
Function / homology | Function and homology information late endosome lumen / positive regulation of T-helper 17 cell lineage commitment / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / regulation of tyrosine phosphorylation of STAT protein / natural killer cell activation involved in immune response / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis ...late endosome lumen / positive regulation of T-helper 17 cell lineage commitment / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / regulation of tyrosine phosphorylation of STAT protein / natural killer cell activation involved in immune response / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of natural killer cell activation / negative regulation of vascular endothelial growth factor signaling pathway / positive regulation of smooth muscle cell apoptotic process / positive regulation of tissue remodeling / positive regulation of lymphocyte proliferation / positive regulation of activation of Janus kinase activity / tissue remodeling / sexual reproduction / positive regulation of T-helper 1 type immune response / positive regulation of NK T cell activation / positive regulation of mononuclear cell proliferation / interleukin-12 receptor binding / positive regulation of memory T cell differentiation / natural killer cell activation / T-helper cell differentiation / negative regulation of interleukin-17 production / positive regulation of osteoclast differentiation / Interleukin-23 signaling / positive regulation of T-helper 17 type immune response / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / positive regulation of neutrophil chemotaxis / positive regulation of granulocyte macrophage colony-stimulating factor production / response to UV-B / Interleukin-12 signaling / cytokine receptor activity / T-helper 1 type immune response / negative regulation of interleukin-10 production / cytokine binding / defense response to protozoan / positive regulation of interleukin-17 production / Interleukin-10 signaling / positive regulation of natural killer cell proliferation / positive regulation of interleukin-10 production / positive regulation of activated T cell proliferation / negative regulation of protein secretion / positive regulation of cell adhesion / T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of defense response to virus by host / regulation of cytokine production / negative regulation of inflammatory response to antigenic stimulus / positive regulation of T cell proliferation / positive regulation of interleukin-12 production / cytokine activity / negative regulation of smooth muscle cell proliferation / cellular response to type II interferon / positive regulation of inflammatory response / positive regulation of T cell mediated cytotoxicity / positive regulation of non-canonical NF-kappaB signal transduction / cytokine-mediated signaling pathway / positive regulation of type II interferon production / cell migration / positive regulation of tumor necrosis factor production / defense response to virus / Interleukin-4 and Interleukin-13 signaling / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / receptor complex / inflammatory response / protein heterodimerization activity / endoplasmic reticulum lumen / external side of plasma membrane / innate immune response / protein-containing complex binding / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | |||||||||
Authors | Wei, A. / Sheriff, S. | |||||||||
Citation | Journal: Structure / Year: 2012 Title: Structures of adnectin/protein complexes reveal an expanded binding footprint. Authors: Ramamurthy, V. / Krystek, S.R. / Bush, A. / Wei, A. / Emanuel, S.L. / Das Gupta, R. / Janjua, A. / Cheng, L. / Murdock, M. / Abramczyk, B. / Cohen, D. / Lin, Z. / Morin, P. / Davis, J.H. / ...Authors: Ramamurthy, V. / Krystek, S.R. / Bush, A. / Wei, A. / Emanuel, S.L. / Das Gupta, R. / Janjua, A. / Cheng, L. / Murdock, M. / Abramczyk, B. / Cohen, D. / Lin, Z. / Morin, P. / Davis, J.H. / Dabritz, M. / McLaughlin, D.C. / Russo, K.A. / Chao, G. / Wright, M.C. / Jenny, V.A. / Engle, L.J. / Furfine, E. / Sheriff, S. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3qwr.cif.gz | 222.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3qwr.ent.gz | 178.5 KB | Display | PDB format |
PDBx/mmJSON format | 3qwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/3qwr ftp://data.pdbj.org/pub/pdb/validation_reports/qw/3qwr | HTTPS FTP |
---|
-Related structure data
Related structure data | 3qwqC 1fnfS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 34739.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL12B, NKSF2 / Plasmid: PFBDUAL / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: P29460 |
---|---|
#2: Protein | Mass: 18696.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL23A, SGRF, UNQ2498/PRO5798 / Plasmid: PFBDUAL / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q9NPF7 |
#3: Protein | Mass: 12479.787 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET9 PCT734 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174 |
#4: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.68 % |
---|---|
Crystal grow | Temperature: 293 K / pH: 7 Details: 0.1 M Tris-HCl, 1 M tri-sodium citrate, 0.2 M NaCl, pH 7.0, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 31, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→42.48 Å / Num. obs: 12835 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 85.75 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 3.25→3.37 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.2 / % possible all: 99.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IL-23 FROM UNPUBLISHED STRUCTURE AND ADNECTIN FROM PDB ENTRY 1FNF RESIDUES 1421-1437, 1444-1466, 1470-1491, 1502-1509 Resolution: 3.25→42.48 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.885 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.47
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 100.73 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.74 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.25→42.48 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.25→3.56 Å / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|