+Open data
-Basic information
Entry | Database: PDB / ID: 1if1 | ||||||
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Title | INTERFERON REGULATORY FACTOR 1 (IRF-1) COMPLEX WITH DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / COMPLEX (DNA-BINDING PROTEIN-DNA) / TRANSCRIPTION FACTOR / INTERFERON REGULATION / HELIX-TURN-HELIX / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information CD8-positive, alpha-beta T cell differentiation / regulation of MyD88-dependent toll-like receptor signaling pathway / regulation of cell cycle => GO:0051726 / positive regulation of natural killer cell differentiation / : / regulation of CD8-positive, alpha-beta T cell proliferation / regulation of adaptive immune response / positive regulation of T-helper 1 cell differentiation / negative regulation of tyrosine phosphorylation of STAT protein / negative regulation of regulatory T cell differentiation ...CD8-positive, alpha-beta T cell differentiation / regulation of MyD88-dependent toll-like receptor signaling pathway / regulation of cell cycle => GO:0051726 / positive regulation of natural killer cell differentiation / : / regulation of CD8-positive, alpha-beta T cell proliferation / regulation of adaptive immune response / positive regulation of T-helper 1 cell differentiation / negative regulation of tyrosine phosphorylation of STAT protein / negative regulation of regulatory T cell differentiation / negative regulation of T-helper 2 cell differentiation / chromatin => GO:0000785 / response to growth hormone / cellular response to peptide hormone stimulus / immune system process / regulation of innate immune response / positive regulation of type I interferon production / canonical NF-kappaB signal transduction / cellular response to interferon-beta / cellular response to interleukin-1 / type II interferon-mediated signaling pathway / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / cellular response to mechanical stimulus / cellular response to tumor necrosis factor / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / defense response to virus / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å | ||||||
Authors | Escalante, C.R. / Yie, J. / Thanos, D. / Aggarwal, A. | ||||||
Citation | Journal: Nature / Year: 1998 Title: Structure of IRF-1 with bound DNA reveals determinants of interferon regulation. Authors: Escalante, C.R. / Yie, J. / Thanos, D. / Aggarwal, A.K. #1: Journal: FEBS Lett. / Year: 1997 Title: Expression, Purification, and Co-Crystallization of Irf-1 Bound to the Interferon-Beta Element Prdi Authors: Escalante, C.R. / Yie, J. / Thanos, D. / Aggarwal, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1if1.cif.gz | 78.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1if1.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 1if1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1if1_validation.pdf.gz | 388.9 KB | Display | wwPDB validaton report |
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Full document | 1if1_full_validation.pdf.gz | 448.1 KB | Display | |
Data in XML | 1if1_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 1if1_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/1if1 ftp://data.pdbj.org/pub/pdb/validation_reports/if/1if1 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper: (Code: given Matrix: (-0.823802, 0.55224, -0.127987), Vector: |
-Components
#1: DNA chain | Mass: 7986.177 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Protein | Mass: 13419.605 Da / Num. of mol.: 2 / Fragment: DNA-BINDING PROTEIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line: MOUSE FIBROBLAST L929 / Plasmid: PET-3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P15314 #3: 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: 3.1 Å3/Da / Density % sol: 60 % | |||||||||||||||
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Crystal grow | pH: 6.5 Details: PROTEIN WAS CRYSTALLIZED FROM 18-22% PEG8K, 300 MM AMMONIUM ACETATE (PH 6.5), 10% GLYCEROL. | |||||||||||||||
Crystal | *PLUS | |||||||||||||||
Crystal grow | *PLUS Method: unknown / Details: Escalante, C.R., (1997) FEBS Lett., 414, 219. | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 111 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jun 1, 1996 / Details: DUAL SLITS |
Radiation | Monochromator: SILICON CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 20328 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 3→3.23 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 13.5 / Rsym value: 0.09 / % possible all: 99.7 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / Num. obs: 21657 / % possible obs: 99.1 % / Num. measured all: 125805 |
Reflection shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.23 Å / % possible obs: 99.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3→12 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 29.97 Å2
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Refinement step | Cycle: LAST / Resolution: 3→12 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 12 Å / σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 29.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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