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Open data
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Basic information
Entry | Database: PDB / ID: 5tqy | |||||||||||||||
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Title | CryoEM reconstruction of human IKK1, closed conformation 3 | |||||||||||||||
![]() | Inhibitor of nuclear factor kappa-B kinase subunit alpha | |||||||||||||||
![]() | TRANSFERASE / kinase / conserved helix-loop-helix / transcription / oncogene | |||||||||||||||
Function / homology | ![]() response to acetate / IkappaB kinase / IkappaB kinase activity / IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / response to cholecystokinin / IkappaB kinase complex / I-kappaB phosphorylation / transferrin receptor binding / IkBA variant leads to EDA-ID ...response to acetate / IkappaB kinase / IkappaB kinase activity / IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / response to cholecystokinin / IkappaB kinase complex / I-kappaB phosphorylation / transferrin receptor binding / IkBA variant leads to EDA-ID / CD40 receptor complex / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / RIP-mediated NFkB activation via ZBP1 / response to hydroperoxide / AKT phosphorylates targets in the cytosol / non-canonical NF-kappaB signal transduction / toll-like receptor 4 signaling pathway / negative regulation of NF-kappaB transcription factor activity / Constitutive Signaling by AKT1 E17K in Cancer / TRAF6 mediated NF-kB activation / positive regulation of interferon-alpha production / Rho protein signal transduction / skeletal muscle contraction / cellular response to cadmium ion / anatomical structure morphogenesis / response to amino acid / canonical NF-kappaB signal transduction / striated muscle cell differentiation / tumor necrosis factor-mediated signaling pathway / 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 / TNFR1-induced NF-kappa-B signaling pathway / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / cellular response to reactive oxygen species / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / response to virus / PKR-mediated signaling / cytoplasmic side of plasma membrane / response to toxic substance / cellular response to virus / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Interleukin-1 signaling / Downstream TCR signaling / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / ER-Phagosome pathway / scaffold protein binding / response to lipopolysaccharide / protein kinase activity / response to xenobiotic stimulus / inflammatory response / immune response / protein heterodimerization activity / protein phosphorylation / innate immune response / protein serine/threonine kinase activity / positive regulation of DNA-templated transcription / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / nucleoplasm / ATP binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.2 Å | |||||||||||||||
![]() | Lyumkis, D. / Ghosh, G. / Polley, S. / Biswath, T. / Huang, D. / Passos, D.O. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for the Activation of IKK1/α. Authors: Smarajit Polley / Dario Oliveira Passos / De-Bin Huang / Maria Carmen Mulero / Anup Mazumder / Tapan Biswas / Inder M Verma / Dmitry Lyumkis / Gourisankar Ghosh / ![]() Abstract: Distinct signaling pathways activate the NF-κB family of transcription factors. The canonical NF-κB-signaling pathway is mediated by IκB kinase 2/β (IKK2/β), while the non-canonical pathway ...Distinct signaling pathways activate the NF-κB family of transcription factors. The canonical NF-κB-signaling pathway is mediated by IκB kinase 2/β (IKK2/β), while the non-canonical pathway depends on IKK1/α. The structural and biochemical bases for distinct signaling by these otherwise highly similar IKKs are unclear. We report single-particle cryoelectron microscopy (cryo-EM) and X-ray crystal structures of human IKK1 in dimeric (∼150 kDa) and hexameric (∼450 kDa) forms. The hexamer, which is the representative form in the crystal but comprises only ∼2% of the particles in solution by cryo-EM, is a trimer of IKK1 dimers. While IKK1 hexamers are not detectable in cells, the surface that supports hexamer formation is critical for IKK1-dependent cellular processing of p100 to p52, the hallmark of non-canonical NF-κB signaling. Comparison of this surface to that in IKK2 indicates significant divergence, and it suggests a fundamental role for this surface in signaling by these kinases through distinct pathways. | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 215.7 KB | Display | ![]() |
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PDB format | ![]() | 172.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8438MC ![]() 8436C ![]() 8437C ![]() 8439C ![]() 5ebzC ![]() 5tqwC ![]() 5tqxC M: map data used to model this data 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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Components
#1: Protein | Mass: 75146.945 Da / Num. of mol.: 2 / Mutation: S176E, S180E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Inhibitor of KappaB Kinase 1 dimer / Type: COMPLEX / Details: dimer / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.15 MDa / Experimental value: YES | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 277 K Details: Sample containing IKK1 dimers in SEC buffer was applied onto freshly plasma-treated (6 seconds, Gatan Solarus plasma cleaner) holey carbon C-flat grids (Protochips), adsorbed for 30 seconds, ...Details: Sample containing IKK1 dimers in SEC buffer was applied onto freshly plasma-treated (6 seconds, Gatan Solarus plasma cleaner) holey carbon C-flat grids (Protochips), adsorbed for 30 seconds, and then plunged into liquid ethane using a manual cryo-plunger in an ambient environment of 4 degrees C. |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Calibrated magnification: 38167 X / Calibrated defocus min: 1100 nm / Calibrated defocus max: 5200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 70 K / Temperature (min): 70 K |
Image recording | Average exposure time: 10 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2918 Details: The dose was fractionated over 50 raw frames collected over a 10 second exposure time (200 ms per frame) on the Gatan K2 Summit direct detection device, with each frame receiving a dose of ...Details: The dose was fractionated over 50 raw frames collected over a 10 second exposure time (200 ms per frame) on the Gatan K2 Summit direct detection device, with each frame receiving a dose of ~6.5 e-/pixel/sec. 2918 movies were collected and recorded at a nominal magnification of 22,500, corresponding to a pixel size of 1.31 A at the specimen level. The individual frames were gain-corrected, then aligned and summed using a GPU-enabled whole frame alignment program (Li et al., 2013), and exposure-filtered (Grant and Grigorieff, 2015). |
Image scans | Sampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 50 / Used frames/image: 1-50 |
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Processing
Software | Name: PHENIX / Version: dev_2499: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Details: within Relion and Frealign / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 230242 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23505 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 340 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: FSC 0.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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