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Yorodumi- PDB-1k1a: Crystal structure of the ankyrin repeat domain of Bcl-3: a unique... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k1a | ||||||
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Title | Crystal structure of the ankyrin repeat domain of Bcl-3: a unique member of the IkappaB protein family | ||||||
Components | B-cell lymphoma 3-encoded protein | ||||||
Keywords | TRANSCRIPTION / Bcl-3 / NF-kappaB transcription factors / IkappaB proteins | ||||||
Function / homology | Function and homology information Bcl3-Bcl10 complex / follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / regulation of DNA binding / marginal zone B cell differentiation / regulation of non-canonical NF-kappaB signal transduction / T cell apoptotic process / negative regulation of interleukin-8 production / germinal center formation / negative regulation of receptor signaling pathway via JAK-STAT ...Bcl3-Bcl10 complex / follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / regulation of DNA binding / marginal zone B cell differentiation / regulation of non-canonical NF-kappaB signal transduction / T cell apoptotic process / negative regulation of interleukin-8 production / germinal center formation / negative regulation of receptor signaling pathway via JAK-STAT / humoral immune response mediated by circulating immunoglobulin / negative regulation of T cell apoptotic process / antimicrobial humoral response / T-helper 2 cell differentiation / response to UV-C / T-helper 1 type immune response / negative regulation of NF-kappaB transcription factor activity / defense response to protozoan / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / DNA damage response, signal transduction by p53 class mediator / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / canonical NF-kappaB signal transduction / spleen development / extracellular matrix organization / positive regulation of translation / response to virus / protein import into nucleus / histone deacetylase binding / transcription corepressor activity / positive regulation of type II interferon production / protein-macromolecule adaptor activity / midbody / regulation of apoptotic process / DNA-binding transcription factor binding / transcription coactivator activity / defense response to bacterium / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / DNA damage response / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Michel, F. / Soler-Lopez, M. / Petosa, C. / Cramer, P. / Siebenlist, U. / Mueller, C.W. | ||||||
Citation | Journal: EMBO J. / Year: 2001 Title: Crystal structure of the ankyrin repeat domain of Bcl-3: a unique member of the IkappaB protein family. Authors: Michel, F. / Soler-Lopez, M. / Petosa, C. / Cramer, P. / Siebenlist, U. / Muller, C.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k1a.cif.gz | 59.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k1a.ent.gz | 43.1 KB | Display | PDB format |
PDBx/mmJSON format | 1k1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/1k1a ftp://data.pdbj.org/pub/pdb/validation_reports/k1/1k1a | HTTPS FTP |
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-Related structure data
Related structure data | 1k1bC 1iknS C: citing same article (ref.) S: Starting model for refinement |
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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: 25829.451 Da / Num. of mol.: 1 / Fragment: ankyrin repeat domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P20749 |
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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: 1.99 Å3/Da / Density % sol: 38.12 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 6000, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5.8 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 28, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. all: 17021 / Num. obs: 17021 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rsym value: 0.072 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.73 % / Mean I/σ(I) obs: 1.65 / Num. unique all: 1479 / Rsym value: 0.697 / % possible all: 77.8 |
Reflection | *PLUS Lowest resolution: 40 Å / Redundancy: 2.71 % / Num. measured all: 46088 / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS % possible obs: 77.8 % / Rmerge(I) obs: 0.697 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ikn Resolution: 1.86→20 Å / SU B: 3.68115 / SU ML: 0.11055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18488 / ESU R Free: 0.15154 / Stereochemistry target values: Engh & Huber Details: RESIDUES SER178,VAL179,LEU182,GLN251,ARG269,SER307 PRESENT DOUBLE CONFORMATIONS.
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Displacement parameters | Biso mean: 21.105 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.199 | ||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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