+Open data
-Basic information
Entry | Database: PDB / ID: 1gji | ||||||
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Title | Crystal structure of c-Rel bound to DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / NF-kB-DNA COMPLEX / TRANSCRIPTION FACTOR / c-Rel HOMODIMER / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information apoptotic DNA fragmentation / non-canonical NF-kappaB signal transduction / canonical NF-kappaB signal transduction / response to cytokine / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / DNA-binding transcription factor activity / innate immune response / chromatin binding ...apoptotic DNA fragmentation / non-canonical NF-kappaB signal transduction / canonical NF-kappaB signal transduction / response to cytokine / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / DNA-binding transcription factor activity / innate immune response / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / molecular replacement, MIR / Resolution: 2.85 Å | ||||||
Authors | Huang, D.B. / Chen, Y.Q. / Ruetsche, M. / Phelps, C.B. / Ghosh, G. | ||||||
Citation | Journal: Structure / Year: 2001 Title: X-ray crystal structure of proto-oncogene product c-Rel bound to the CD28 response element of IL-2. Authors: Huang, D.B. / Chen, Y.Q. / Ruetsche, M. / Phelps, C.B. / Ghosh, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gji.cif.gz | 159 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gji.ent.gz | 127.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gji_validation.pdf.gz | 384.1 KB | Display | wwPDB validaton report |
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Full document | 1gji_full_validation.pdf.gz | 427.1 KB | Display | |
Data in XML | 1gji_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 1gji_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/1gji ftp://data.pdbj.org/pub/pdb/validation_reports/gj/1gji | 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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-Components
#1: DNA chain | Mass: 6206.054 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 6058.939 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 31894.316 Da / Num. of mol.: 2 / Fragment: Rel homology region Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: P16236 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 63 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 7.5 Details: PEG 4000, spermine, DTT, pH 7.5, EVAPORATION, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 168 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Feb 14, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→25 Å / Num. all: 21455 / Num. obs: 18723 / % possible obs: 90.8 % / Observed criterion σ(F): 2 / Redundancy: 10 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 7 % / Rmerge(I) obs: 0.424 / Num. unique all: 1159 / % possible all: 46 |
Reflection | *PLUS Num. obs: 21455 / % possible obs: 90 % / Num. measured all: 215187 / Rmerge(I) obs: 0.086 |
Reflection shell | *PLUS % possible obs: 48 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement, MIR Starting model: p65/DNA complex Resolution: 2.85→25 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: The DNA molecule has alternate conformations. Two sets of coordinates for the DNA molecule were refined with 0.5 occupancy each.
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Refinement step | Cycle: LAST / Resolution: 2.85→25 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.227 / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.227 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.0079 |