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Open data
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Basic information
Entry | Database: PDB / ID: 1my5 | ||||||
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Title | NF-kappaB p65 subunit dimerization domain homodimer | ||||||
![]() | NF-kappaB p65 (RelA) subunit | ||||||
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Function / homology | ![]() SUMOylation of immune response proteins / 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 / TRAF6 mediated NF-kB activation / 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 ...SUMOylation of immune response proteins / 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 / TRAF6 mediated NF-kB activation / 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 / FCERI mediated NF-kB activation / positive regulation of chondrocyte differentiation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / acetaldehyde metabolic process / Downstream TCR signaling / prolactin signaling pathway / NF-kappaB p50/p65 complex / positive regulation of Schwann cell differentiation / CD209 (DC-SIGN) signaling / cellular response to peptidoglycan / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
Model details | transcription factor p65 | ||||||
![]() | Huxford, T. / Mishler, D. / Phelps, C.B. / Huang, D.-B. / Sengchanthalangsy, L.L. / Reeves, R. / Hughes, C.A. / Komives, E.A. / Ghosh, G. | ||||||
![]() | ![]() Title: Solvent exposed non-contacting amino acids play a critical role in NF-kappaB/I kappaB alpha complex formation Authors: Huxford, T. / Mishler, D. / Phelps, C.B. / Huang, D.-B. / Sengchanthalangsy, L.L. / Reeves, R. / Hughes, C.A. / Komives, E.A. / Ghosh, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.8 KB | Display | ![]() |
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PDB format | ![]() | 41.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1my7C ![]() 1bftS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 13201.880 Da / Num. of mol.: 2 / Fragment: residues 191-304 (dimerization domain) 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: 2.18 Å3/Da / Density % sol: 43.47 % | ||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M sodium HEPES, 0.2M sodium tartrate, 2M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 22, 2001 / Details: Osmic optics |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→30 Å / Num. all: 21911 / Num. obs: 20531 / % possible obs: 93.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.6 % / Rsym value: 0.053 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 3 / % possible all: 58 |
Reflection | *PLUS Num. measured all: 114510 / Rmerge(I) obs: 0.053 |
Reflection shell | *PLUS % possible obs: 58 % |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: pdb id 1bft Resolution: 1.8→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 30 Å / Rfactor Rwork![]() | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |