+Open data
-Basic information
Entry | Database: PDB / ID: 3s9d | ||||||
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Title | binary complex between IFNa2 and IFNAR2 | ||||||
Components |
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Keywords | SIGNALING PROTEIN/RECEPTOR / human / type I interferons / IFNa2 / IFNAR2 / sub-complex of the interferon signaling complex / SIGNALING PROTEIN-RECEPTOR complex | ||||||
Function / homology | Function and homology information type I interferon receptor activity / type I interferon binding / interleukin-22 receptor activity / type I interferon receptor binding / JAK pathway signal transduction adaptor activity / cell surface receptor signaling pathway via STAT / negative regulation of interleukin-5 production / response to interferon-beta / negative regulation of interleukin-13 production / negative regulation of T cell differentiation ...type I interferon receptor activity / type I interferon binding / interleukin-22 receptor activity / type I interferon receptor binding / JAK pathway signal transduction adaptor activity / cell surface receptor signaling pathway via STAT / negative regulation of interleukin-5 production / response to interferon-beta / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / natural killer cell activation involved in immune response / response to interferon-alpha / positive regulation of peptidyl-serine phosphorylation of STAT protein / negative regulation of T-helper 2 cell cytokine production / T cell activation involved in immune response / negative regulation of viral entry into host cell / TRAF6 mediated IRF7 activation / type I interferon-mediated signaling pathway / B cell proliferation / response to exogenous dsRNA / cytokine binding / cell surface receptor signaling pathway via JAK-STAT / humoral immune response / Regulation of IFNA/IFNB signaling / cellular response to interferon-beta / B cell differentiation / cytokine activity / response to virus / Evasion by RSV of host interferon responses / cellular response to virus / cytokine-mediated signaling pathway / Interferon alpha/beta signaling / Factors involved in megakaryocyte development and platelet production / cell-cell signaling / Potential therapeutics for SARS / collagen-containing extracellular matrix / defense response to virus / adaptive immune response / cell surface receptor signaling pathway / inflammatory response / negative regulation of gene expression / negative regulation of DNA-templated transcription / protein kinase binding / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9999 Å | ||||||
Authors | Thomas, C. / Garcia, K.C. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2011 Title: Structural linkage between ligand discrimination and receptor activation by type I interferons. Authors: Thomas, C. / Moraga, I. / Levin, D. / Krutzik, P.O. / Podoplelova, Y. / Trejo, A. / Lee, C. / Yarden, G. / Vleck, S.E. / Glenn, J.S. / Nolan, G.P. / Piehler, J. / Schreiber, G. / Garcia, K.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s9d.cif.gz | 146.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s9d.ent.gz | 114.2 KB | Display | PDB format |
PDBx/mmJSON format | 3s9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3s9d_validation.pdf.gz | 459.4 KB | Display | wwPDB validaton report |
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Full document | 3s9d_full_validation.pdf.gz | 467.2 KB | Display | |
Data in XML | 3s9d_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 3s9d_validation.cif.gz | 39.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s9/3s9d ftp://data.pdbj.org/pub/pdb/validation_reports/s9/3s9d | HTTPS FTP |
-Related structure data
Related structure data | 3s8wSC 3s98C 3se3C 3se4C 1rh2S 2hymS S: Starting model for refinement C: citing same article (ref.) |
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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: 19393.232 Da / Num. of mol.: 2 / Fragment: IFNa2 (UNP Residues 24-188) / Mutation: H57A, E58A, Q61A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IFNA2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01563 #2: Protein | Mass: 22797.992 Da / Num. of mol.: 2 / Fragment: UNP Residues 37-232 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IFNAR2, IFNABR, IFNARB / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P48551 #3: Chemical | ChemComp-CL / | #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: 2.74 Å3/Da / Density % sol: 55.05 % |
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Crystal grow | Temperature: 293 K Details: 20% (w/v) PEG 3350, 200 mM NaSCN, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 5, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9999→19.897 Å / Num. obs: 61371 / % possible obs: 99.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 31.2 Å2 / Rsym value: 0.05 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.9999→2.1 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.6 / Rsym value: 53.6 / % possible all: 99.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 3S8W, 2HYM, and 1RH2 Resolution: 1.9999→19.897 Å / σ(F): 1.99 / 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 / Bsol: 59.98 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9999→19.897 Å
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Refine LS restraints |
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LS refinement shell |
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