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- PDB-3brv: NEMO/IKKb association domain structure -

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Basic information

Entry
Database: PDB / ID: 3brv
TitleNEMO/IKKb association domain structure
Components
  • Inhibitor of nuclear factor kappa-B kinase subunit beta
  • NF-kappa-B essential modulator
KeywordsTRANSFERASE/TRANSCRIPTION / NEMO / IKK-gamma / FIP3 / IKKAP1 / NF-kB essential modulator / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Transferase / Disease mutation / Ectodermal dysplasia / Host-virus interaction / Nucleus / Transcription / Transcription regulation / TRANSFERASE-TRANSCRIPTION COMPLEX
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 / establishment of vesicle localization / linear polyubiquitin binding / negative regulation of myosin-light-chain-phosphatase activity / negative regulation of bicellular tight junction assembly ...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 / establishment of vesicle localization / linear polyubiquitin binding / 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 / positive regulation of ubiquitin-dependent protein catabolic process / SUMOylation of immune response proteins / regulation of establishment of endothelial barrier / regulation of tumor necrosis factor-mediated signaling pathway / anoikis / MyD88-dependent toll-like receptor signaling pathway / interleukin-1-mediated signaling pathway / K63-linked polyubiquitin modification-dependent protein binding / cortical actin cytoskeleton organization / positive regulation of T cell receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / Fc-epsilon receptor signaling pathway / TRAF6 mediated NF-kB activation / positive regulation of macroautophagy / protein maturation / polyubiquitin modification-dependent protein binding / canonical NF-kappaB signal transduction / signaling adaptor activity / stress-activated MAPK cascade / ubiquitin ligase complex / 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 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TNFR1-induced NF-kappa-B signaling pathway / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / 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 / mitotic spindle / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / spindle pole / Interleukin-1 signaling / Ovarian tumor domain proteases / 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 / protein-containing complex assembly / peptidyl-serine phosphorylation / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / Ub-specific processing proteases / protein kinase activity / defense response to bacterium / inflammatory response / immune response / membrane raft / protein heterodimerization activity / protein domain specific binding / protein phosphorylation / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / ubiquitin protein ligase binding / DNA damage response / 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 / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2110 / L1 transposable element, trimerization 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 / C2H2 type zinc-finger / NF-kappa-B essential modulator NEMO, N-terminal ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2110 / L1 transposable element, trimerization 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 / C2H2 type zinc-finger / NF-kappa-B essential modulator NEMO, N-terminal / NF-kappa-B essential modulator NEMO / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / NF-kappa-B essential modulator NEMO, CC2-LZ domain / Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Inhibitor of nuclear factor kappa-B kinase subunit beta / NF-kappa-B essential modulator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSilvian, L.F.
CitationJournal: Structure / Year: 2008
Title: Structure of a NEMO/IKK-Associating Domain Reveals Architecture of the Interaction Site.
Authors: Rushe, M. / Silvian, L. / Bixler, S. / Chen, L.L. / Cheung, A. / Bowes, S. / Cuervo, H. / Berkowitz, S. / Zheng, T. / Guckian, K. / Pellegrini, M. / Lugovskoy, A.
History
DepositionDec 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: NF-kappa-B essential modulator
C: Inhibitor of nuclear factor kappa-B kinase subunit beta
D: NF-kappa-B essential modulator


Theoretical massNumber of molelcules
Total (without water)27,9414
Polymers27,9414
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint-88.6 kcal/mol
Surface area11570 Å2
MethodPISA
2
A: Inhibitor of nuclear factor kappa-B kinase subunit beta
B: NF-kappa-B essential modulator


Theoretical massNumber of molelcules
Total (without water)13,9712
Polymers13,9712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-16.8 kcal/mol
Surface area8440 Å2
MethodPISA
3
C: Inhibitor of nuclear factor kappa-B kinase subunit beta
D: NF-kappa-B essential modulator


Theoretical massNumber of molelcules
Total (without water)13,9712
Polymers13,9712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-16.6 kcal/mol
Surface area8490 Å2
MethodPISA
4
A: Inhibitor of nuclear factor kappa-B kinase subunit beta
D: NF-kappa-B essential modulator


Theoretical massNumber of molelcules
Total (without water)13,9712
Polymers13,9712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-16.9 kcal/mol
Surface area8230 Å2
MethodPISA
5
B: NF-kappa-B essential modulator
C: Inhibitor of nuclear factor kappa-B kinase subunit beta


Theoretical massNumber of molelcules
Total (without water)13,9712
Polymers13,9712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-15.8 kcal/mol
Surface area8440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.820, 50.670, 102.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 5436.988 Da / Num. of mol.: 2 / Fragment: NEMO-binding / Source method: obtained synthetically
Details: peptide synthesized corresponds to residues 701-746 of IKK-beta kinase
References: UniProt: O14920, IkappaB kinase
#2: Protein NF-kappa-B essential modulator / NEMO / NF-kappa-B essential modifier / Inhibitor of nuclear factor kappa-B kinase subunit gamma / ...NEMO / NF-kappa-B essential modifier / Inhibitor of nuclear factor kappa-B kinase subunit gamma / IkB kinase subunit gamma / I-kappa-B kinase gamma / IKK-gamma / IKKG / IkB kinase-associated protein 1 / IKKAP1 / FIP-3


Mass: 8533.713 Da / Num. of mol.: 2 / Fragment: UNP residues 44-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IKBKG, FIP3, NEMO / Plasmid: pet11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y6K9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% Peg 4K, 0.1M Tris pH 8.5, 0.2M MgCl2, 10mM DTT, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2005 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 12480 / Num. obs: 12363 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 15.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 2.2 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.45 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.889 / SU B: 14.36 / SU ML: 0.2 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29396 594 4.8 %RANDOM
Rwork0.20824 ---
obs0.21225 11737 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.169 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--0.05 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1616 0 0 103 1719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0211640
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.241.9572212
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3385202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24725.28189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.41315302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.261513
X-RAY DIFFRACTIONr_chiral_restr0.1510.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021237
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2570.2796
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21134
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2550.292
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2841.51058
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.05621609
X-RAY DIFFRACTIONr_scbond_it3.5263661
X-RAY DIFFRACTIONr_scangle_it5.2054.5602
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 42 -
Rwork0.251 813 -
obs--95.32 %
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)
11.6529-0.5513-3.670729.3272-9.272511.93270.7659-1.79910.2291.0181-0.38651.0064-1.08311.0249-0.37950.1269-0.00130.04070.311-0.07970.0143-24.008-9.17825.377
216.35516.7925-11.09632.8527-4.49837.9120.25640.42030.89690.00560.18590.2615-0.2925-0.1618-0.44220.18190.05320.023-0.01180.00110.1359-8.824-0.36911.183
312.3961-4.1615-3.50487.07365.76174.69440.25080.6290.9185-0.4548-0.0277-0.0486-0.57720.1141-0.22320.10910.0049-0.0164-0.01430.0832-0.042210.3099.025-4.674
421.27141.4997-13.2835.7689-3.15759.16570.360.54910.44330.23730.65321.0048-0.2275-0.8257-1.01320.05030.00620.04630.21450.19810.1523-36.08-16.95422.21
530.7489.6663-15.6193.8301-4.78728.2188-0.0140.35050.0704-0.05830.20250.1505-0.1101-0.2944-0.18850.03770.0008-0.046-0.01460.046-0.0247-7.949-7.13.463
618.759111.2257-0.72159.21-3.9094.879-0.9811.6032-0.8812-0.84160.6462-1.52920.7056-0.40770.33480.1519-0.0730.11440.0714-0.11280.174221.4091.664-7.516
716.243412.9281-11.631519.1041-1.342415.43640.50361.9017-1.36870.9599-0.02610.29360.7551-2.6415-0.47750.0671-0.0962-0.04290.3779-0.01670.1622-25.576-22.80912.819
822.44388.9745-0.525914.121-1.45610.1597-0.2223-0.3953-0.69070.1037-0.0104-0.7490.03870.1490.23270.04070.0334-0.0126-0.047-0.0163-0.116-7.182-15.42310.386
910.03961.8083-6.4599.9803-2.17417.7459-0.0039-0.2988-0.13980.1057-0.2867-0.38630.10160.10330.29060.08820.0459-0.02950.01880.02910.019116.541-4.0234.292
1028.351419.9793-6.625618.5405-5.25051.7511-0.11261.0631-0.4424-0.1670.4055-0.0565-0.0519-0.2814-0.29290.02910.00150.04070.14490.0428-0.039-31.411-24.20924.571
1123.160111.0343-12.14745.5945-6.39597.46850.0933-0.1254-0.24830.0597-0.107-0.0238-0.1105-0.06940.01370.02970.04420.0186-0.0369-0.0386-0.0264-2.993-6.12216.126
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A705 - 713
2X-RAY DIFFRACTION2A714 - 734
3X-RAY DIFFRACTION3A735 - 742
4X-RAY DIFFRACTION4B49 - 65
5X-RAY DIFFRACTION5B66 - 96
6X-RAY DIFFRACTION6B97 - 109
7X-RAY DIFFRACTION7C702 - 713
8X-RAY DIFFRACTION8C714 - 729
9X-RAY DIFFRACTION9C730 - 743
10X-RAY DIFFRACTION10D49 - 65
11X-RAY DIFFRACTION11D66 - 95

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