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- EMDB-8438: CryoEM reconstruction of human IKK1, closed conformation 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-8438
TitleCryoEM reconstruction of human IKK1, closed conformation 3
Map dataCryoEM reconstruction of human IKK1, closed conformation 3, final map
Sample
  • Complex: Inhibitor of KappaB Kinase 1 dimer
    • Protein or peptide: Inhibitor of nuclear factor kappa-B kinase subunit alpha
Keywordskinase / 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 / SLC15A4:TASL-dependent IRF5 activation / IkappaB kinase complex / 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 / SLC15A4:TASL-dependent IRF5 activation / IkappaB kinase complex / 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 / non-canonical NF-kappaB signal transduction / AKT phosphorylates targets in the cytosol / response to hydroperoxide / toll-like receptor 4 signaling pathway / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of NF-kappaB transcription factor activity / TRAF6 mediated NF-kB activation / positive regulation of interferon-alpha production / anatomical structure morphogenesis / skeletal muscle contraction / canonical NF-kappaB signal transduction / response to amino acid / tumor necrosis factor-mediated signaling pathway / striated muscle cell differentiation / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / TICAM1, RIP1-mediated IKK complex recruitment / MAP3K8 (TPL2)-dependent MAPK1/3 activation / IKK complex recruitment mediated by RIP1 / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / TNFR1-induced NF-kappa-B signaling pathway / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / Regulation of TNFR1 signaling / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / PKR-mediated signaling / response to virus / CLEC7A (Dectin-1) signaling / cellular response to virus / FCERI mediated NF-kB activation / response to toxic substance / cytoplasmic side of plasma membrane / Interleukin-1 signaling / Downstream TCR signaling / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / scaffold protein binding / positive regulation of canonical NF-kappaB signal transduction / protein kinase activity / immune response / inflammatory response / response to xenobiotic stimulus / protein heterodimerization activity / innate immune response / protein serine/threonine kinase activity / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / cytosol / cytoplasm
Similarity search - Function
I-kappa-kinase-beta NEMO binding domain / IKBKB, scaffold dimerization domain / IKBKB, scaffold dimerization domain superfamily / I-kappa-kinase-beta NEMO binding domain / IQBAL scaffold dimerization domain / I-kappa-kinase-beta NEMO binding domain / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...I-kappa-kinase-beta NEMO binding domain / IKBKB, scaffold dimerization domain / IKBKB, scaffold dimerization domain superfamily / I-kappa-kinase-beta NEMO binding domain / IQBAL scaffold dimerization domain / I-kappa-kinase-beta NEMO binding domain / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Inhibitor of nuclear factor kappa-B kinase subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsLyumkis D / Ghosh G
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorDP5 OD021396-01 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI064326 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA141722 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071862 United States
CitationJournal: 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
DepositionOct 24, 2016-
Header (metadata) releaseNov 9, 2016-
Map releaseNov 9, 2016-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5tqy
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8438.png

Downloads & links

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Map

FileDownload / File: emd_8438.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM reconstruction of human IKK1, closed conformation 3, final map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 192 pix.
= 251.52 Å		1.31 Å/pix.
x 192 pix.
= 251.52 Å		1.31 Å/pix.
x 192 pix.
= 251.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.07057655 - 0.19414972
Average (Standard dev.)0.00045486656 (±0.008565027)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 251.51999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z251.520251.520251.520
α/β/γ90.00090.00090.000
start NX/NY/NZ-54-3-120
NX/NY/NZ12323205
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0710.1940.000

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Supplemental data

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Half map: CryoEM reconstruction of human IKK1, closed conformation 3,...

Fileemd_8438_half_map_1.map
AnnotationCryoEM reconstruction of human IKK1, closed conformation 3, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM reconstruction of human IKK1, closed conformation 3,...

Fileemd_8438_half_map_2.map
AnnotationCryoEM reconstruction of human IKK1, closed conformation 3, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Inhibitor of KappaB Kinase 1 dimer

EntireName: Inhibitor of KappaB Kinase 1 dimer
Components
  • Complex: Inhibitor of KappaB Kinase 1 dimer
    • Protein or peptide: Inhibitor of nuclear factor kappa-B kinase subunit alpha

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Supramolecule #1: Inhibitor of KappaB Kinase 1 dimer

SupramoleculeName: Inhibitor of KappaB Kinase 1 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: dimer
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: Inhibitor of nuclear factor kappa-B kinase subunit alpha

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.146945 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMC4H12ClNO3Tris-HCl
5.0 mMC4H10O2S2DTT
5.0 %C3H8O3Glycerol
GridModel: 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
VitrificationCryogen 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..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 230242
Startup modelType of model: INSILICO MODEL
Details: common lines model generated using OptiMod and EMAN1
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9.11) / Number images used: 23505
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN (ver. 9.11)
Final 3D classificationNumber classes: 3 / Software - Name: FREALIGN (ver. 9.11)
Details: Three conformational states were captured using a four-model classification, with the last class corresponding to particles that produced a low-resolution reconstruction (increasing this ...Details: Three conformational states were captured using a four-model classification, with the last class corresponding to particles that produced a low-resolution reconstruction (increasing this number to 5 or 6 classes did not increase the number of recovered conformational states). Although three conformational states were recovered during classification, it is likely these states are not discrete, and a continuum of movement about the central hinge exists, which is indicated by the relatively homogeneous distribution of particles within the classes.
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 340 / Target criteria: FSC 0.5
Output model

PDB-5tqy:
CryoEM reconstruction of human IKK1, closed conformation 3

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