+Open data
-Basic information
Entry | Database: PDB / ID: 1zka | ||||||
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Title | NF-kB RelB forms an intertwined homodimer, Y300S mutant | ||||||
Components | Transcription factor RelB | ||||||
Keywords | TRANSCRIPTION / Transcription factors / intertwined dimer / NF-kB dimerization | ||||||
Function / homology | Function and homology information T-helper 1 cell differentiation / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / lymphocyte differentiation / CD209 (DC-SIGN) signaling / myeloid dendritic cell differentiation / negative regulation of interferon-beta production / cellular response to osmotic stress / T-helper 1 type immune response / non-canonical NF-kappaB signal transduction ...T-helper 1 cell differentiation / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / lymphocyte differentiation / CD209 (DC-SIGN) signaling / myeloid dendritic cell differentiation / negative regulation of interferon-beta production / cellular response to osmotic stress / T-helper 1 type immune response / non-canonical NF-kappaB signal transduction / antigen processing and presentation / canonical NF-kappaB signal transduction / transcription repressor complex / response to cytokine / circadian regulation of gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / centrosome / negative regulation of DNA-templated transcription / synapse / chromatin / protein kinase binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Huang, D.B. / Vu, D. / Ghosh, G. | ||||||
Citation | Journal: Structure / Year: 2005 Title: NF-kappaB RelB forms an intertwined homodimer. Authors: Huang, D.B. / Vu, D. / Ghosh, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zka.cif.gz | 35.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zka.ent.gz | 23.4 KB | Display | PDB format |
PDBx/mmJSON format | 1zka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/1zka ftp://data.pdbj.org/pub/pdb/validation_reports/zk/1zka | HTTPS FTP |
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-Related structure data
Related structure data | 1zk9SC 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: 12323.943 Da / Num. of mol.: 1 / Fragment: dimerization domain / Mutation: Y300S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Relb / Plasmid: PET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q04863 |
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#2: 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: 4.46 Å3/Da / Density % sol: 71 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000,AS, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Jan 1, 2002 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 10657 / Num. obs: 8784 / % possible obs: 86 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 12 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2 / Num. unique all: 628 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb ID 1zk9 Resolution: 2.2→29.23 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 534187.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.32 Å2 / ksol: 0.343717 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→29.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.059 / Total num. of bins used: 6
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Xplor file |
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