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Open data
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Basic information
Entry | Database: PDB / ID: 6xx0 | ||||||
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Title | Crystal structure of NEMO in complex with Ubv-LIN | ||||||
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![]() | PROTEIN BINDING / Inhibitor / Ubiquitin | ||||||
Function / homology | ![]() IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / IkappaB kinase complex / establishment of vesicle localization / linear polyubiquitin binding / transferrin receptor binding / IkBA variant leads to EDA-ID / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / RIP-mediated NFkB activation via ZBP1 / positive regulation of ubiquitin-dependent protein catabolic process ...IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / IkappaB kinase complex / establishment of vesicle localization / linear polyubiquitin binding / transferrin receptor binding / IkBA variant leads to EDA-ID / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / RIP-mediated NFkB activation via ZBP1 / positive regulation of ubiquitin-dependent protein catabolic process / SUMOylation of immune response proteins / anoikis / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of T cell receptor signaling pathway / TRAF6 mediated NF-kB activation / positive regulation of macroautophagy / polyubiquitin modification-dependent protein binding / canonical NF-kappaB signal transduction / signaling adaptor activity / ubiquitin ligase complex / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TNFR1-induced NF-kappa-B signaling pathway / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / response to virus / PKR-mediated signaling / mitotic spindle / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / spindle pole / Interleukin-1 signaling / Ovarian tumor domain proteases / Downstream TCR signaling / kinase activity / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / ER-Phagosome pathway / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / defense response to bacterium / inflammatory response / immune response / protein heterodimerization activity / protein domain specific binding / phosphorylation / innate immune response / apoptotic process / ubiquitin protein ligase binding / DNA damage response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Akutsu, M. / Skenderovic, A. / Garcia-Pardo, J. / Maculins, T. / Dikic, I. | ||||||
![]() | ![]() Title: Discovery of Protein-Protein Interaction Inhibitors by Integrating Protein Engineering and Chemical Screening Platforms. Authors: Maculins, T. / Garcia-Pardo, J. / Skenderovic, A. / Gebel, J. / Putyrski, M. / Vorobyov, A. / Busse, P. / Varga, G. / Kuzikov, M. / Zaliani, A. / Rahighi, S. / Schaeffer, V. / Parnham, M.J. ...Authors: Maculins, T. / Garcia-Pardo, J. / Skenderovic, A. / Gebel, J. / Putyrski, M. / Vorobyov, A. / Busse, P. / Varga, G. / Kuzikov, M. / Zaliani, A. / Rahighi, S. / Schaeffer, V. / Parnham, M.J. / Sidhu, S.S. / Ernst, A. / Dotsch, V. / Akutsu, M. / Dikic, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.3 KB | Display | ![]() |
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PDB format | ![]() | 56.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.5 KB | Display | ![]() |
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Full document | ![]() | 450.8 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 19.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6yekC ![]() 3f89S 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
#1: Protein | Mass: 10331.796 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 8949.163 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 22.5% polyethylene glycol 3350, 0.1M Magnesium chloride, 0.1M Try-HCl, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 25, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→44.99 Å / Num. obs: 101221 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.997 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.6→2.74 Å / Num. unique obs: 2213 / CC1/2: 0.548 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3f89 Resolution: 2.6→40.42 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.893 / SU B: 13.093 / SU ML: 0.267 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.52 / ESU R Free: 0.333 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.01 Å2 / Biso mean: 53.685 Å2 / Biso min: 16.95 Å2
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Refinement step | Cycle: final / Resolution: 2.6→40.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.668 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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