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- PDB-4e3c: X-ray crystal structure of human IKK2 in an active conformation -

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Basic information

Entry
Database: PDB / ID: 4e3c
TitleX-ray crystal structure of human IKK2 in an active conformation
ComponentsInhibitor of nuclear factor kappa-B kinase subunit beta
KeywordsTRANSFERASE / Kanase / auto-phosphorylation / NEMO binding
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 / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / TRIF-dependent toll-like receptor signaling pathway / regulation of phosphorylation / RIP-mediated NFkB activation via ZBP1 / 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 / Fc-epsilon receptor signaling pathway / stimulatory C-type lectin 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 / Regulation of TNFR1 signaling / Activation of NF-kappaB in B cells / response to virus / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / 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 / ER-Phagosome pathway / T cell receptor signaling 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 / protein serine kinase activity / innate immune response / 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 / Ubiquitin-like (UB roll) ...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
Inhibitor of nuclear factor kappa-B kinase subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.98 Å
AuthorsPolley, S. / Huang, D.B. / Hauenstein, A.V. / Ghosh, G. / Huxford, T.
CitationJournal: Plos.Biol. / Year: 2013
Title: X-ray crystal structure of human IKK2 in an active conformation
Authors: Polley, S. / Huang, D.B. / Hauenstein, A.V. / Fusco, A.J. / Zhong, X. / Vu, D. / Hoffmann, A. / Verma, I.V. / Ghosh, G. / Huaford, T.
History
DepositionMar 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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


Theoretical massNumber of molelcules
Total (without water)462,9816
Polymers462,9816
Non-polymers00
Water0
1
A: Inhibitor of nuclear factor kappa-B kinase subunit beta
F: Inhibitor of nuclear factor kappa-B kinase subunit beta


Theoretical massNumber of molelcules
Total (without water)154,3272
Polymers154,3272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-18 kcal/mol
Surface area65060 Å2
MethodPISA
2
B: Inhibitor of nuclear factor kappa-B kinase subunit beta
C: Inhibitor of nuclear factor kappa-B kinase subunit beta


Theoretical massNumber of molelcules
Total (without water)154,3272
Polymers154,3272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-20 kcal/mol
Surface area63580 Å2
MethodPISA
3
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)154,3272
Polymers154,3272
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-20 kcal/mol
Surface area64490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.810, 170.810, 509.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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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: 77163.523 Da / Num. of mol.: 6 / Fragment: UNP Residues 11-669 / Mutation: S177E, S181E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IKBKB, IKKB / Plasmid: pFastBac HTb / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: O14920, IkappaB 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: 4.01 Å3/Da / Density % sol: 69.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.2M sodium malonate, 250mM ammonium acetate, 10mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 97 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Jan 1, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.98→30 Å / Num. all: 63535 / Num. obs: 53076 / % possible obs: 81 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 6.4
Reflection shellResolution: 3.98→4.12 Å / Redundancy: 4 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.73 / % possible all: 97.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QA8

3qa8


Resolution: 3.98→29.84 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 27933.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.299 2032 3.8 %RANDOM
Rwork0.267 ---
obs0.267 53076 81 %-
all-63535 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 93.5303 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 140.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å20 Å2
2--1.27 Å20 Å2
3----2.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.67 Å0.59 Å
Luzzati d res low-5 Å
Luzzati sigma a1.04 Å1.05 Å
Refinement stepCycle: LAST / Resolution: 3.98→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30416 0 0 0 30416
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 3.98→4.23 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.393 246 3.4 %
Rwork0.376 6951 -
obs--67.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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