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- PDB-8omv: Crystal structure of the constitutively active S117E/S181E mutant... -

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Basic information

Entry
Database: PDB / ID: 8omv
TitleCrystal structure of the constitutively active S117E/S181E mutant of human IKK2
ComponentsInhibitor of nuclear factor kappa-B kinase subunit beta
KeywordsTRANSFERASE / IKK / NF-kappaB / IkBa / docking
Function / homology
Function and homology information


antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / IkappaB kinase / IkappaB kinase activity / IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / IkappaB kinase complex / negative regulation of myosin-light-chain-phosphatase activity / negative regulation of bicellular tight junction assembly / transferrin receptor binding / IkBA variant leads to EDA-ID ...antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / IkappaB kinase / IkappaB kinase activity / IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / IkappaB kinase complex / negative regulation of myosin-light-chain-phosphatase activity / negative regulation of bicellular tight junction assembly / transferrin receptor binding / IkBA variant leads to EDA-ID / toll-like receptor 3 signaling pathway / CD40 receptor complex / TRIF-dependent toll-like receptor signaling pathway / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / RIP-mediated NFkB activation via ZBP1 / regulation of phosphorylation / regulation of establishment of endothelial barrier / regulation of tumor necrosis factor-mediated signaling pathway / MyD88-dependent toll-like receptor signaling pathway / interleukin-1-mediated signaling pathway / cortical actin cytoskeleton organization / stimulatory C-type lectin receptor signaling pathway / Fc-epsilon receptor signaling pathway / TRAF6 mediated NF-kB activation / protein maturation / canonical NF-kappaB signal transduction / stress-activated MAPK cascade / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / tumor necrosis factor-mediated signaling pathway / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / 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 / Regulation of NF-kappa B signaling / protein localization to plasma membrane / 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 / cytoplasmic side of plasma membrane / 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 / T cell receptor signaling pathway / ER-Phagosome pathway / scaffold protein binding / peptidyl-serine phosphorylation / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / protein kinase activity / inflammatory response / membrane raft / protein heterodimerization activity / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
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 / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...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 / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Inhibitor of nuclear factor kappa-B kinase subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.16 Å
AuthorsMcEwen, A.G. / Li, C. / Moro, S. / Poussin-Courmontagne, P. / Zanier, K.
Funding support France, 3items
OrganizationGrant numberCountry
Instruct-ERIC Center (Strasbourg Centre)PID: 11382 France
Agence Nationale de la Recherche (ANR)ANR-13-JSV8-0004-01 France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05-01 France
CitationJournal: To be published
Title: A novel YDD(phi)X(phi) linear motif mediates docking of IKK catalytic dimers to NF-kappaB substrates: structural and functional insights
Authors: Li, C. / Moro, S. / Shastak, K. / O'Reily, F. / Donzeau, M. / Graziadei, A. / McEwen, A.G. / Poussin-Courmontagne, P. / Bachelart, T. / Fiskin, M. / Berrodier, N. / Orfanoudakis, G. / ...Authors: Li, C. / Moro, S. / Shastak, K. / O'Reily, F. / Donzeau, M. / Graziadei, A. / McEwen, A.G. / Poussin-Courmontagne, P. / Bachelart, T. / Fiskin, M. / Berrodier, N. / Orfanoudakis, G. / Poterszman, A. / Torbeev, V. / Rappsilber, J. / Davy, N. / Chariot, A. / Zanier, K.
History
DepositionMar 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inhibitor of nuclear factor kappa-B kinase subunit beta
B: Inhibitor of nuclear factor kappa-B kinase subunit beta
C: Inhibitor of nuclear factor kappa-B kinase subunit beta
D: Inhibitor of nuclear factor kappa-B kinase subunit beta
E: Inhibitor of nuclear factor kappa-B kinase subunit beta


Theoretical massNumber of molelcules
Total (without water)387,0445
Polymers387,0445
Non-polymers00
Water00
1
A: Inhibitor of nuclear factor kappa-B kinase subunit beta
B: Inhibitor of nuclear factor kappa-B kinase subunit beta


Theoretical massNumber of molelcules
Total (without water)154,8182
Polymers154,8182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Inhibitor of nuclear factor kappa-B kinase subunit beta
D: Inhibitor of nuclear factor kappa-B kinase subunit beta


Theoretical massNumber of molelcules
Total (without water)154,8182
Polymers154,8182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Inhibitor of nuclear factor kappa-B kinase subunit beta

E: Inhibitor of nuclear factor kappa-B kinase subunit beta


Theoretical massNumber of molelcules
Total (without water)154,8182
Polymers154,8182
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)226.293, 136.802, 204.358
Angle α, β, γ (deg.)90.00, 91.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Inhibitor of nuclear factor kappa-B kinase subunit beta / I-kappa-B-kinase beta / IKK-B / IKK-beta / IkBKB / I-kappa-B kinase 2 / IKK2 / Nuclear factor NF- ...I-kappa-B-kinase beta / IKK-B / IKK-beta / IkBKB / I-kappa-B kinase 2 / IKK2 / Nuclear factor NF-kappa-B inhibitor kinase beta / NFKBIKB / Serine/threonine protein kinase IKBKB


Mass: 77408.781 Da / Num. of mol.: 5 / Mutation: S177E, S181E
Source method: isolated from a genetically manipulated source
Details: residues 1-699 / Source: (gene. exp.) Homo sapiens (human) / Gene: IKBKB, IKKB / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O14920, IkappaB kinase, non-specific serine/threonine protein kinase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.06 Å3/Da / Density % sol: 69.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6M (NH4)2SO4, 0.1M Bis-Tris HCl pH 6.5, 10% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 16, 2019
Details: a convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors
RadiationMonochromator: Channel cut crystal monochromator (Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 4.14→63.25 Å / Num. obs: 47432 / % possible obs: 99.1 % / Redundancy: 6.99 % / CC1/2: 0.995 / Rmerge(I) obs: 0.275 / Rrim(I) all: 0.298 / Net I/σ(I): 3.67
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
4.14-4.399.9972780.0411.0561
4.39-4.695.14272110.1695.5671
4.69-5.062.94367110.453.1641
5.06-5.542.47662090.4882.6641
5.54-6.191.89756120.5352.0461
6.19-7.130.95249580.7961.0351
7.13-8.710.23642380.990.2541
8.71-12.20.06933020.9970.0751
12.2-63.250.06519130.9960.0731

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.16→63.25 Å / SU ML: 0.72 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 45.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2991 1018 4.97 %RANDOM
Rwork0.2571 ---
obs0.2592 20474 43.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.16→63.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25125 0 0 0 25125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00225541
X-RAY DIFFRACTIONf_angle_d0.56934491
X-RAY DIFFRACTIONf_dihedral_angle_d3.3453351
X-RAY DIFFRACTIONf_chiral_restr0.0383875
X-RAY DIFFRACTIONf_plane_restr0.0034474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.16-4.380.530520.3619166X-RAY DIFFRACTION3
4.38-4.650.3947210.3425589X-RAY DIFFRACTION9
4.65-5.010.3096630.29491215X-RAY DIFFRACTION19
5.01-5.520.3017880.30781885X-RAY DIFFRACTION29
5.52-6.310.40352000.32923298X-RAY DIFFRACTION52
6.31-7.950.3443060.30685811X-RAY DIFFRACTION91
7.95-63.250.26213380.21896492X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.05630.03230.00440.15230.04370.00350.1285-0.1313-0.07731.0251-0.3223-0.96960.46861.2354-0.01051.60530.4278-0.56582.07730.35171.487225.478910.685882.5152
20.10240.06180.06380.49720.13950.0551-0.1380.3897-0.311-0.1084-0.30510.19850.39930.2359-0.43281.88830.48241.56882.44160.2252.998622.58347.444256.614
31.58670.4402-0.16320.1275-0.13311.0535-0.42130.4232-0.2677-0.9858-0.083-1.10590.22460.063-0.00231.25780.04770.36281.34050.60672.025227.263151.082752.7886
40.08070.43190.08370.28030.093-0.0869-0.1822-0.00910.4917-0.021-0.28690.2466-0.24920.596-0.00641.4964-0.411-0.45452.2309-0.4851.972219.390155.90853.5693
50.52560.4384-0.00690.5888-0.1430.49090.1364-0.36320.57530.51890.12640.4995-0.1808-0.22140.8119-0.4167-0.42450.48160.1292-0.2759-0.0653-47.144971.698946.4366
60.38510.1925-0.10540.096-0.2918-0.0370.4067-0.7308-0.80610.622-0.37-0.44170.41070.94-0.19660.7639-0.802-0.08591.3130.12211.1378-0.89280.819967.7931
70.0858-0.0954-0.09510.11530.14470.1393-0.1702-0.7503-0.58590.20490.1849-0.6528-0.53570.3322-0.00012.3714-0.88870.5822.9876-0.10981.749744.419462.066178.8609
80.78390.4294-0.38080.3754-0.20570.18560.45520.4133-0.0192-0.19880.68950.16990.5061-0.00430.2823.9247-1.5217-1.4333.9826-0.25562.790347.246265.3554103.8548
90.1835-0.2372-0.11470.52640.14350.05740.2585-0.5354-1.0711.8608-0.3333-0.0396-0.02350.2544-0.0222.1639-0.3864-0.7073.2942-0.05492.427935.789642.0356108.971
100.506-0.5006-0.37750.44290.35160.2401-0.0487-0.4729-0.6543-0.05380.24350.29370.7919-0.7241-0.00023.6538-0.4570.13653.32020.36153.386712.832238.1767109.8061
110.57710.30740.30140.15350.11190.5666-0.84080.1221-1.07570.36680.40280.12621.53260.7853-0.04431.51880.68430.02952.28270.44262.243125.24399.270612.3957
120.6970.1650.27090.7091-0.09920.60770.2454-0.0952-0.14740.67010.00130.1919-0.00180.7654-0.17320.35440.4047-0.26391.41030.1550.692-12.264524.984727.6935
130.67410.1652-0.3605-0.0308-0.27380.4394-0.33320.06220.31520.49930.35180.1023-0.48050.41170.26421.10920.1396-0.22941.79050.25461.6449-21.285735.394126.7931
140.30910.1189-0.58680.4705-0.22431.07280.3496-0.71590.02770.7089-0.46-0.17390.19940.839-1.17630.7917-0.214-0.1351.2106-0.72891.4482-33.254229.013528.6987
150.168-0.1121-0.17240.4117-0.3910.77930.2339-0.22590.27-0.26220.18360.50070.1892-0.15741.9121-0.5982-0.47050.0051-0.2521-0.65660.2318-1.230896.492427.5345
160.48-0.04950.02430.47560.35920.7504-0.3966-0.0786-0.14770.2385-0.3030.48040.5348-0.5141-2.9829-0.12330.1656-0.0975-0.1565-0.09030.2077-22.069762.830812.4655
170.56360.20390.06981.3372-0.3730.783-0.32920.0256-0.0929-0.3683-0.0514-1.2460.373-0.0927-0.79310.8078-0.183-0.1660.612-0.40551.5615-51.85734.50528.038
180.599-0.3616-0.30821.01160.53390.30280.5019-0.0557-0.19570.03470.5368-0.1140.4985-0.62240.39291.1547-0.65-0.30711.67130.23560.84279.431167.59220.3929
190.0495-0.06630.01180.1786-0.0470.0705-0.12350.06810.1617-0.1449-0.1909-0.5668-0.11910.0143-1.570.64830.37810.33770.320.20850.9946-36.666148.567610.532
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 12 through 186 )
2X-RAY DIFFRACTION2chain 'C' and (resid 187 through 266 )
3X-RAY DIFFRACTION3chain 'C' and (resid 267 through 551 )
4X-RAY DIFFRACTION4chain 'C' and (resid 552 through 664 )
5X-RAY DIFFRACTION5chain 'D' and (resid 6 through 307 )
6X-RAY DIFFRACTION6chain 'D' and (resid 308 through 665 )
7X-RAY DIFFRACTION7chain 'E' and (resid 9 through 182 )
8X-RAY DIFFRACTION8chain 'E' and (resid 183 through 266 )
9X-RAY DIFFRACTION9chain 'E' and (resid 267 through 422 )
10X-RAY DIFFRACTION10chain 'E' and (resid 423 through 643 )
11X-RAY DIFFRACTION11chain 'A' and (resid 8 through 327 )
12X-RAY DIFFRACTION12chain 'A' and (resid 328 through 500 )
13X-RAY DIFFRACTION13chain 'A' and (resid 501 through 587 )
14X-RAY DIFFRACTION14chain 'A' and (resid 588 through 666 )
15X-RAY DIFFRACTION15chain 'B' and (resid 8 through 327 )
16X-RAY DIFFRACTION16chain 'B' and (resid 328 through 499 )
17X-RAY DIFFRACTION17chain 'B' and (resid 500 through 549 )
18X-RAY DIFFRACTION18chain 'B' and (resid 550 through 587 )
19X-RAY DIFFRACTION19chain 'B' and (resid 588 through 664 )

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