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- PDB-1u41: Crystal structure of YLGV mutant of dimerisation domain of NF-kB ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1u41 | ||||||
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Title | Crystal structure of YLGV mutant of dimerisation domain of NF-kB p50 transcription factor | ||||||
![]() | Nuclear factor NF-kappa-B p105 subunit | ||||||
![]() | TRANSCRIPTION / TRANSCRIPTION FACTOR / NF-KB / DIMERIZATION DOMAIN / INTERTWINED FOLDING | ||||||
Function / homology | ![]() cellular response to diterpene / cellular response to glucoside / Regulated proteolysis of p75NTR / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TRAF6 mediated NF-kB activation / positive regulation of hyaluronan biosynthetic process / NF-kB is activated and signals survival ...cellular response to diterpene / cellular response to glucoside / Regulated proteolysis of p75NTR / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TRAF6 mediated NF-kB activation / positive regulation of hyaluronan biosynthetic process / NF-kB is activated and signals survival / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / cellular response to carbohydrate stimulus / antibacterial innate immune response / mammary gland involution / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / cellular response to interleukin-17 / Downstream TCR signaling / NF-kappaB p50/p65 complex / cellular response to peptide / CD209 (DC-SIGN) signaling / negative regulation of interleukin-12 production / cellular response to interleukin-6 / cellular response to dsRNA / actinin binding / cellular response to angiotensin / negative regulation of cytokine production / positive regulation of miRNA metabolic process / non-canonical NF-kappaB signal transduction / cellular response to cytokine stimulus / cellular response to organic cyclic compound / cellular response to interleukin-1 / positive regulation of transcription initiation by RNA polymerase II / lymph node development / canonical NF-kappaB signal transduction / JNK cascade / cellular response to brain-derived neurotrophic factor stimulus / heat shock protein binding / response to muscle stretch / Neutrophil degranulation / response to cytokine / RNA polymerase II transcription regulatory region sequence-specific DNA binding / B cell receptor signaling pathway / transcription coregulator activity / response to organic cyclic compound / cellular response to virus / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / cellular response to nicotine / cellular response to mechanical stimulus / MAPK cascade / sequence-specific double-stranded DNA binding / positive regulation of canonical Wnt signaling pathway / cellular response to tumor necrosis factor / gene expression / double-stranded DNA binding / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / response to oxidative stress / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / protein-containing complex binding / chromatin / negative regulation of apoptotic process / apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chirgadze, D.Y. / Demydchuk, M. / Becker, M. / Moran, S. / Paoli, M. | ||||||
![]() | ![]() Title: Snapshot of Protein Structure Evolution Reveals Conservation of Functional Dimerization through Intertwined Folding Authors: Chirgadze, D.Y. / Demydchuk, M. / Becker, M. / Moran, S. / Paoli, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102 KB | Display | ![]() |
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PDB format | ![]() | 79.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1u36C ![]() 1u3jC ![]() 1u3yC ![]() 1u3zC ![]() 1u42C ![]() 1bfsS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | CHAINS A AND B COMPRIZE THE BIOLOGICAL DIMER / CHAINS C AND D COMPRIZE THE BIOLOGICAL DIMER |
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Components
#1: Protein | Mass: 12242.806 Da / Num. of mol.: 4 / Fragment: dimerization domain / Mutation: A308G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 36.7 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, ammonium sulphate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2002 / Details: OSMIC MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / 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→69.01 Å / Num. all: 20980 / Num. obs: 20980 / % possible obs: 98.3 % / Observed criterion σ(I): 2.5 / Redundancy: 5.1 % / Biso Wilson estimate: 29.295 Å2 / Rsym value: 0.065 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.2→2.25 Å / Rmerge(I) obs: 0.281 / % possible all: 96 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BFS Resolution: 2.202→69.01 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.194 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.332 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.24 Å2
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Refinement step | Cycle: LAST / Resolution: 2.202→69.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.202→2.259 Å / Total num. of bins used: 20 /
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