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Yorodumi- EMDB-8437: CryoEM reconstruction of human IKK1, intermediate conformation 2 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8437 | |||||||||||||||
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Title | CryoEM reconstruction of human IKK1, intermediate conformation 2 | |||||||||||||||
Map data | CryoEM reconstruction of human IKK1, intermediate conformation 2, final map | |||||||||||||||
Sample |
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Keywords | kinase / conserved helix-loop-helix / transcription / oncogene / TRANSFERASE | |||||||||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.4 Å | |||||||||||||||
Authors | Lyumkis D / Ghosh G | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Cell Rep / Year: 2016 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8437.map.gz | 24.8 MB | EMDB map data format | |
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Header (meta data) | emd-8437-v30.xml emd-8437.xml | 22.5 KB 22.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8437_fsc.xml | 6.8 KB | Display | FSC data file |
Images | emd_8437.png | 149.8 KB | ||
Filedesc metadata | emd-8437.cif.gz | 7.3 KB | ||
Others | emd_8437_half_map_1.map.gz emd_8437_half_map_2.map.gz | 5.6 MB 5.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8437 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8437 | HTTPS FTP |
-Validation report
Summary document | emd_8437_validation.pdf.gz | 797 KB | Display | EMDB validaton report |
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Full document | emd_8437_full_validation.pdf.gz | 796.6 KB | Display | |
Data in XML | emd_8437_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | emd_8437_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8437 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8437 | HTTPS FTP |
-Related structure data
Related structure data | 5tqxMC 8436C 8438C 8439C 5ebzC 5tqwC 5tqyC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8437.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM reconstruction of human IKK1, intermediate conformation 2, final map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: CryoEM reconstruction of human IKK1, intermediate conformation 2,...
File | emd_8437_half_map_1.map | ||||||||||||
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Annotation | CryoEM reconstruction of human IKK1, intermediate conformation 2, unmasked half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: CryoEM reconstruction of human IKK1, intermediate conformation 2,...
File | emd_8437_half_map_2.map | ||||||||||||
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Annotation | CryoEM reconstruction of human IKK1, intermediate conformation 2, unmasked half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Inhibitor of KappaB Kinase 1 dimer
Entire | Name: Inhibitor of KappaB Kinase 1 dimer |
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Components |
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-Supramolecule #1: Inhibitor of KappaB Kinase 1 dimer
Supramolecule | Name: Inhibitor of KappaB Kinase 1 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: dimer |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 150 KDa |
-Macromolecule #1: Inhibitor of nuclear factor kappa-B kinase subunit alpha
Macromolecule | Name: Inhibitor of nuclear factor kappa-B kinase subunit alpha type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: IkappaB kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 75.146945 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: DPEFGAGGPW EMRERLGTGG FGNVCLYQHR ELDLKIAIKS CRLELSTKNR ERWCHEIQIM KKLNHANVVK ACDVPEELNI LIHDVPLLA MEYCSGGDLR KLLNKPENCC GLKESQILSL LSDIGSGIRY LHENKIIHRD LKPENIVLQD VGGKIIHKII D LGYAKDVD ...String: DPEFGAGGPW EMRERLGTGG FGNVCLYQHR ELDLKIAIKS CRLELSTKNR ERWCHEIQIM KKLNHANVVK ACDVPEELNI LIHDVPLLA MEYCSGGDLR KLLNKPENCC GLKESQILSL LSDIGSGIRY LHENKIIHRD LKPENIVLQD VGGKIIHKII D LGYAKDVD QGELCTEFVG TLQYLAPELF ENKPYTATVD YWSFGTMVFE CIAGYRPFLH HLQPFTWHEK IKKKDPKCIF AC EEMSGEV RFSSHLPQPN SLCSLIVEPM ENWLQLMLNW DPQQRGGPVD LTLKQPRCFV LMDHILNLKI VHILNMTSAK IIS FLLPPD ESLHSLQSRI ERETGINTGS QELLSETGIS LDPRKPASQC VLDGVRGCDS YMVYLFDKSK TVYEGPFASR SLSD CVNYI VQDSKIQLPI IQLRKVWAEA VHYVSGLKED YSRLFQGQRA AMLSLLRYNA NLTKMKNTLI SASQQLKAKL EFFHK SIQL DLERYSEQMT YGISSEKMLK AWKEMEEKAI HYAEVGVIGY LEDQIMSLHA EIMELQKSPY GRRQGDLMES LEQRAI DLY KQLKHRPSDH SYSDSTEMVK IIVHTVQSQD RVLKELFGHL SKLLGCKQKI IDLLPKVEVA LSNIKEADNT VMFMQGK RQ KEIWHLLKIA CTQ UniProtKB: Inhibitor of nuclear factor kappa-B kinase subunit alpha |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.5 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 6 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER 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.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 70.0 K / Max: 70.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 2918 / Average exposure time: 10.0 sec. / Average electron dose: 40.0 e/Å2 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). |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 5.2 µm / Calibrated defocus min: 1.1 µm / Calibrated magnification: 38167 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 340 / Target criteria: FSC 0.5 |
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Output model | PDB-5tqx: |