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- PDB-4kik: Human IkB kinase beta -

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Basic information

Entry
Database: PDB / ID: 4kik
TitleHuman IkB kinase beta
Components(Inhibitor of nuclear factor kappa-B kinase subunit beta) x 2
KeywordsTRANSFERASE / kinase / NkB signaling
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 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 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 / interleukin-1-mediated signaling pathway / MyD88-dependent toll-like receptor 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 / tumor necrosis factor-mediated signaling pathway / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / 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 / protein heterodimerization activity / membrane raft / 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 / cytosol / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #250 / 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 / : / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #250 / 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 / : / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
K-252A / Inhibitor of nuclear factor kappa-B kinase subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsLiu, S. / Mosyak, L.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Crystal Structure of a Human I kappa B Kinase beta Asymmetric Dimer.
Authors: Liu, S. / Misquitta, Y.R. / Olland, A. / Johnson, M.A. / Kelleher, K.S. / Kriz, R. / Lin, L.L. / Stahl, M. / Mosyak, L.
History
DepositionMay 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,5184
Polymers156,5832
Non-polymers9352
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-29 kcal/mol
Surface area63390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.954, 68.689, 107.401
Angle α, β, γ (deg.)90.00, 107.03, 90.00
Int Tables number4
Space group name H-MP1211

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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


Mass: 78251.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IKBKB, IKKB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O14920, IkappaB kinase
#2: 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


Mass: 78331.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IKBKB, IKKB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O14920, IkappaB kinase
#3: Chemical ChemComp-KSA / K-252A


Mass: 467.473 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H21N3O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.78 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→47.2 Å / Num. all: 36644 / Num. obs: 34922 / % possible obs: 95.3 % / Observed criterion σ(I): 1.5 / Redundancy: 2.9 % / Biso Wilson estimate: 67.89 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 10

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Processing

SoftwareName: BUSTER / Version: 2.11.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→47.17 Å / Cor.coef. Fo:Fc: 0.9251 / Cor.coef. Fo:Fc free: 0.8841 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 1742 4.99 %RANDOM
Rwork0.1836 ---
obs0.1863 34922 93.74 %-
Displacement parametersBiso mean: 52.53 Å2
Baniso -1Baniso -2Baniso -3
1--4.6177 Å20 Å2-8.6857 Å2
2---4.4953 Å20 Å2
3---9.113 Å2
Refine analyzeLuzzati coordinate error obs: 0.371 Å
Refinement stepCycle: LAST / Resolution: 2.83→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10301 0 70 221 10592
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110567HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1514294HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5105SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes328HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1537HARMONIC5
X-RAY DIFFRACTIONt_it10567HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion3.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1342SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11841SEMIHARMONIC4
LS refinement shellResolution: 2.83→2.91 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.36 108 5.89 %
Rwork0.2695 1727 -
all0.2748 1835 -
obs--93.74 %
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)
12.32960.0025-0.53971.671-0.09351.97020.097-0.24690.30740.0042-0.06920.0304-0.4304-0.1252-0.0278-0.06370.015-0.0049-0.1005-0.00170.029749.42339.8879-56.5757
21.6008-0.19070.4282.5145-0.80211.92040.0914-0.07220.4289-0.0809-0.09850.1507-0.0366-0.07160.0071-0.1552-0.0007-0.0334-0.033-0.04830.042757.42922.584-57.8655
31.6390.2132-0.55541.4599-0.30761.2743-0.0545-0.0907-0.0515-0.0916-0.0101-0.07350.1520.22240.0646-0.13160.021-0.055-0.0069-0.00290.001565.086210.0472-55.3347
44.67511.71871.82295.4022.81149.6754-0.0320.05610.1467-0.30460.1221-0.1380.13650.5864-0.0901-0.16550.0905-0.0767-0.0283-0.0307-0.223961.65630.9832-85.3866
52.3682.00871.10554.7040.68364.0313-0.05610.098-0.08880.0082-0.00620.34460.03020.06750.0623-0.15080.0479-0.0273-0.04240.00650.063945.3555-2.7843-58.4357
60.00750.1953-0.57660.75011.14543.6853-0.0431-0.0362-0.01860.0990.0925-0.1012-0.0502-0.0619-0.0494-0.09230.101-0.07260.1477-0.0224-0.146145.5626-6.3789-114.8751
73.4820.5868-1.54770.8176-0.4517-1.149-0.02950.03110.05070.00210.01630.14830.0085-0.12880.0131-0.057-0.1201-0.03490.22340.0053-0.218939.8209-11.2406-101.6665
81.3711-0.6-1.89112.1683-2.7956-1.28580.03250.06020.09420.10350.07340.2854-0.0485-0.1288-0.1059-0.27390.0814-0.11350.0567-0.00010.182735.45164.3624-58.2472
91.34420.2063-1.98840.0361-0.872-1.3442-0.0311-0.2338-0.0321-0.4215-0.07950.28190.2872-0.05730.1105-0.0044-0.11660.03340.0389-0.1381-0.061840.25-9.8682-68.9284
10-0.2418-0.54471.63560.15980.69832.4381-0.00630.22990.17910.3775-0.1337-0.01270.04770.020.140.03120.0494-0.12580.0076-0.0308-0.001751.2594-11.4589-106.013
114.4616-0.9469-1.96860.51171.7971-0.10760.02210.209-0.0625-0.019-0.028-0.0628-0.004-0.06040.0059-0.17380.035-0.00570.0527-0.03590.031754.3194-6.6646-144.9826
124.45450.0920.36381.8257-0.96064.5396-0.0326-0.2743-0.2545-0.4041-0.068-0.26890.3054-0.02750.1006-0.0992-0.03910.0321-0.1775-0.01160.0455-16.1118-42.2117-72.4129
130.67040.8229-1.53723.467-0.29152.89140.01470.27430.1137-0.35730.12720.18270.3405-0.2522-0.1419-0.1610.0274-0.0153-0.00670.0449-0.0586-20.1293-24.9395-81.2055
141.86520.3317-0.34423.06350.52172.3776-0.15180.4390.3472-0.18490.30090.4116-0.0637-0.3-0.1492-0.26020.04780.01550.00820.17360.0388-23.967-10.9166-84.4539
157.7163.39870.1313.0766-1.15854.55-0.0730.3640.1058-0.19230.20570.05370.2691-0.4445-0.1327-0.149-0.06840.160.09310.0254-0.2084-0.2336-4.5677-105.1281
161.44570.4333-2.0040.2961-0.82820.7755-0.0440.2141-0.0102-0.04240.0346-0.04710.01650.07280.0095-0.05820.00740.0960.1478-0.0215-0.06013.1486-1.001-86.0791
172.2243-0.2518-1.45040.2742-0.5010.1448-0.0290.07980.14830.068-0.0322-0.1821-0.06160.06130.0612-0.15920.0739-0.03270.12760.0222-0.026543.37770.1867-136.7397
18-0.99681.54821.41590-2.19782.7050.05160.14350.3464-0.0728-0.2810.0322-0.23510.18430.2293-0.1070.10770.13430.06730.16740.038541.87476.6984-144.4573
19-0.39032.15891.61540-0.05192.1569-0.0204-0.0768-0.07280.02120.0312-0.0257-0.00010.0705-0.0108-0.0838-0.03220.03390.2914-0.1364-0.190127.8383.1054-105.5722
201.5078-0.6859-2.46940-0.1193.9567-0.0253-0.0483-0.0120.03930.1278-0.0283-0.13510.2704-0.1026-0.135-0.12240.04680.0854-0.04950.02296.71690.3791-81.6015
215.1086-0.507-0.88050.62810.3908-1.0043-0.0350.41820.1599-0.1478-0.08080.2905-0.08610.06890.1158-0.23870.0656-0.05940.20090.0185-0.073936.6853-3.2863-144.3201
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 100
2X-RAY DIFFRACTION2A101 - 199
3X-RAY DIFFRACTION3A200 - 309
4X-RAY DIFFRACTION4A310 - 394
5X-RAY DIFFRACTION5A400 - 445
6X-RAY DIFFRACTION6A446 - 494
7X-RAY DIFFRACTION7A534 - 550
8X-RAY DIFFRACTION8A558 - 585
9X-RAY DIFFRACTION9A586 - 610
10X-RAY DIFFRACTION10A611 - 637
11X-RAY DIFFRACTION11A638 - 663
12X-RAY DIFFRACTION12B8 - 100
13X-RAY DIFFRACTION13B101 - 199
14X-RAY DIFFRACTION14B200 - 309
15X-RAY DIFFRACTION15B310 - 398
16X-RAY DIFFRACTION16B403 - 470
17X-RAY DIFFRACTION17B471 - 497
18X-RAY DIFFRACTION18B498 - 533
19X-RAY DIFFRACTION19B534 - 550
20X-RAY DIFFRACTION20B558 - 628
21X-RAY DIFFRACTION21B629 - 663

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