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Yorodumi- PDB-1u42: Crystal structure of MLAM mutant of dimerisation domain of NF-kB ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u42 | ||||||
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Title | Crystal structure of MLAM mutant of dimerisation domain of NF-kB p50 transcription factor | ||||||
Components | Nuclear factor NF-kappa-B p105 subunit | ||||||
Keywords | TRANSCRIPTION / TRANSCRIPTION FACTOR / NF-KB / DIMERIZATION DOMAIN / INTERTWINED FOLDING | ||||||
Function / homology | Function and homology information 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 / antibacterial innate immune response / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / cellular response to carbohydrate stimulus / mammary gland involution / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / cellular response to peptide / Downstream TCR signaling / cellular response to interleukin-17 / NF-kappaB p50/p65 complex / CD209 (DC-SIGN) signaling / negative regulation of interleukin-12 production / cellular response to dsRNA / cellular response to interleukin-6 / 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 / positive regulation of transcription initiation by RNA polymerase II / canonical NF-kappaB signal transduction / lymph node development / cellular response to interleukin-1 / JNK cascade / cellular response to brain-derived neurotrophic factor stimulus / heat shock protein binding / response to muscle stretch / Neutrophil degranulation / protein sequestering activity / response to cytokine / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / B cell receptor signaling pathway / 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 mechanical stimulus / cellular response to nicotine / positive regulation of canonical Wnt signaling pathway / MAPK cascade / sequence-specific double-stranded DNA binding / gene expression / cellular response to tumor necrosis factor / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / response to oxidative stress / cellular response to lipopolysaccharide / transcription regulator complex / sequence-specific DNA binding / transcription cis-regulatory region binding / 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 / negative regulation of gene expression / innate immune response / negative regulation of DNA-templated transcription / apoptotic process / chromatin binding / chromatin / protein-containing complex binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of 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 | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.699 Å | ||||||
Authors | Chirgadze, D.Y. / Demydchuk, M. / Becker, M. / Moran, S. / Paoli, M. | ||||||
Citation | Journal: Structure / Year: 2004 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u42.cif.gz | 32.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u42.ent.gz | 21.4 KB | Display | PDB format |
PDBx/mmJSON format | 1u42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/1u42 ftp://data.pdbj.org/pub/pdb/validation_reports/u4/1u42 | HTTPS FTP |
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-Related structure data
Related structure data | 1u36C 1u3jC 1u3yC 1u3zC 1u41C 1bfsS 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: 12256.918 Da / Num. of mol.: 1 / Fragment: dimerization domain / Mutation: Y267M, V310M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nfkb1, 18033 / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P25799 |
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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: 2.32 Å3/Da / Density % sol: 46.5 % |
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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: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.864 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 23, 2002 |
Radiation | Monochromator: DARESBURY / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.864 Å / Relative weight: 1 |
Reflection | Resolution: 2.699→42.26 Å / Num. all: 3233 / Num. obs: 3233 / % possible obs: 99.8 % / Observed criterion σ(I): 2.5 / Redundancy: 7.4 % / Biso Wilson estimate: 75.4 Å2 / Rsym value: 0.042 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.699→2.76 Å / Rmerge(I) obs: 0.347 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BFS Resolution: 2.699→42.26 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.886 / SU B: 23.11 / SU ML: 0.477 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.468 / 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: 56.978 Å2
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Refinement step | Cycle: LAST / Resolution: 2.699→42.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.699→2.769 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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