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Yorodumi- PDB-3og4: The crystal structure of human interferon lambda 1 complexed with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3og4 | |||||||||
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Title | The crystal structure of human interferon lambda 1 complexed with its high affinity receptor in space group P21212 | |||||||||
Components |
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Keywords | CYTOKINE/CYTOKINE RECEPTOR / Helical bundle / fibronectin type III domains / beta-sandwich / Cytokine / cytokine receptor / IL-10R2 / Membrane / CYTOKINE-CYTOKINE RECEPTOR complex | |||||||||
Function / homology | Function and homology information interleukin-28 receptor binding / negative regulation of memory T cell differentiation / response to type III interferon / positive regulation of MHC class I biosynthetic process / interleukin-28 receptor complex / negative regulation of type 2 immune response / negative regulation of interleukin-5 production / mucosal immune response / negative regulation of interleukin-13 production / negative regulation of T cell differentiation ...interleukin-28 receptor binding / negative regulation of memory T cell differentiation / response to type III interferon / positive regulation of MHC class I biosynthetic process / interleukin-28 receptor complex / negative regulation of type 2 immune response / negative regulation of interleukin-5 production / mucosal immune response / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / positive regulation of cellular respiration / type III interferon-mediated signaling pathway / regulation of defense response to virus by host / cytokine receptor activity / Other interleukin signaling / Interleukin-20 family signaling / cell surface receptor signaling pathway via JAK-STAT / positive regulation of tyrosine phosphorylation of STAT protein / cytokine activity / positive regulation of receptor signaling pathway via JAK-STAT / cellular response to virus / cytokine-mediated signaling pathway / positive regulation of type II interferon production / positive regulation of immune response / defense response to virus / negative regulation of cell population proliferation / innate immune response / signaling receptor binding / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / extracellular space / extracellular region / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.16 Å | |||||||||
Authors | Miknis, Z.J. / Magracheva, E. / Lei, W. / Zdanov, A. / Kotenko, S.V. / Wlodawer, A. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Crystal structure of the complex of human interferon-lambda1 with its high affinity receptor interferon-lambdaR1. Authors: Miknis, Z.J. / Magracheva, E. / Li, W. / Zdanov, A. / Kotenko, S.V. / Wlodawer, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3og4.cif.gz | 160.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3og4.ent.gz | 124.1 KB | Display | PDB format |
PDBx/mmJSON format | 3og4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3og4_validation.pdf.gz | 899.6 KB | Display | wwPDB validaton report |
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Full document | 3og4_full_validation.pdf.gz | 906.5 KB | Display | |
Data in XML | 3og4_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 3og4_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/3og4 ftp://data.pdbj.org/pub/pdb/validation_reports/og/3og4 | HTTPS FTP |
-Related structure data
Related structure data | 3og6C 3g9vS 3hhcS 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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Unit cell |
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-Components
#1: Protein | Mass: 19795.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Purchased from Preprotech / Source: (gene. exp.) Homo sapiens (human) / Gene: IFNL1, IL29, ZCYTO21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IU54 |
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#2: Protein | Mass: 25320.770 Da / Num. of mol.: 1 / Fragment: Extracellular domain (UNP residues 19-226) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: hCG_1982865, IL28RA, RP11-10N16.1-001 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: Q5VTX7, UniProt: Q8IU57*PLUS |
#3: Polysaccharide | beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Sugar | ChemComp-NAG / |
#5: 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: 3.48 Å3/Da / Density % sol: 64.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 17% PEG 3350, 100 mM HEPES pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2009 Details: Rosenbaum-Rock monochromator high-resolution double-crystal Si(220) sagittal focusing, Rosenbaum-Rock vertical focusing mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 3.7 % / Av σ(I) over netI: 16.8 / Number: 122399 / Rmerge(I) obs: 0.057 / Χ2: 0.85 / D res high: 2.16 Å / D res low: 30 Å / Num. obs: 33364 / % possible obs: 97.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.16→30 Å / Num. all: 34254 / Num. obs: 33364 / % possible obs: 97.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3HHC and PDB entry 3G9V Resolution: 2.16→29.112 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.77 / σ(F): 0.1 / Phase error: 25.97 / 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: 74.289 Å2 / ksol: 0.331 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.16→29.112 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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