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- PDB-3brt: NEMO/IKK association domain structure -

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Basic information

Entry
Database: PDB / ID: 3brt
TitleNEMO/IKK association domain structure
Components
  • Inhibitor of nuclear factor kappa-B kinase subunit beta,Inhibitor of nuclear factor kappa-B kinase subunit alpha
  • NF-kappa-B essential modulator
KeywordsTransferase/Transcription / NEMO / IKK-gamma / FIP3 / IKKAP1 / NF-kB essential modulator / Acetylation / ATP-binding / Cytoplasm / Kinase / Nucleotide-binding / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase / Transferase / Coiled coil / 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 / 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 / IkappaB kinase complex / SLC15A4:TASL-dependent IRF5 activation / establishment of vesicle localization ...antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / 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 / IkappaB kinase complex / SLC15A4:TASL-dependent IRF5 activation / establishment of vesicle localization / linear polyubiquitin binding / : / I-kappaB phosphorylation / 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 / positive regulation of ubiquitin-dependent protein catabolic process / regulation of establishment of endothelial barrier / SUMOylation of immune response proteins / regulation of phosphorylation / regulation of tumor necrosis factor-mediated signaling pathway / anoikis / AKT phosphorylates targets in the cytosol / interleukin-1-mediated signaling pathway / MyD88-dependent toll-like receptor signaling pathway / non-canonical NF-kappaB signal transduction / response to hydroperoxide / cortical actin cytoskeleton organization / toll-like receptor 4 signaling pathway / negative regulation of NF-kappaB transcription factor activity / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of T cell receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / Constitutive Signaling by AKT1 E17K in Cancer / Fc-epsilon receptor signaling pathway / positive regulation of interferon-alpha production / TRAF6 mediated NF-kB activation / positive regulation of macroautophagy / Rho protein signal transduction / skeletal muscle contraction / protein maturation / polyubiquitin modification-dependent protein binding / anatomical structure morphogenesis / response to amino acid / canonical NF-kappaB signal transduction / signaling adaptor activity / ubiquitin ligase complex / stress-activated MAPK cascade / tumor necrosis factor-mediated signaling pathway / striated muscle cell differentiation / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / cellular response to cadmium ion / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / TNFR1-induced NF-kappa-B signaling pathway / protein localization to plasma membrane / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / 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 / response to virus / NOD1/2 Signaling Pathway / PKR-mediated signaling / cellular response to virus / mitotic spindle / CLEC7A (Dectin-1) signaling / spindle pole / response to toxic substance / FCERI mediated NF-kB activation / cytoplasmic side of plasma membrane / Interleukin-1 signaling / cellular response to reactive oxygen species / 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 / peptidyl-serine phosphorylation / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / response to lipopolysaccharide / non-specific serine/threonine protein kinase / protein kinase activity / Ub-specific processing proteases / defense response to bacterium
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 / 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 / NF-kappa-B essential modulator NEMO, N-terminal / : / NF-kappa-B essential modulator NEMO / C2H2 type zinc-finger / 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, ATP binding site / Protein kinases ATP-binding region signature. / 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 / Inhibitor of nuclear factor kappa-B kinase subunit alpha / NF-kappa-B essential modulator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 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: Version format compliance
Revision 1.2Aug 2, 2017Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Revision 1.3Oct 20, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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


Theoretical massNumber of molelcules
Total (without water)27,1374
Polymers27,1374
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
MethodPISA
2
A: Inhibitor of nuclear factor kappa-B kinase subunit beta,Inhibitor of nuclear factor kappa-B kinase subunit alpha
B: NF-kappa-B essential modulator


Theoretical massNumber of molelcules
Total (without water)13,5682
Polymers13,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
MethodPISA
3
C: Inhibitor of nuclear factor kappa-B kinase subunit beta,Inhibitor of nuclear factor kappa-B kinase subunit alpha
D: NF-kappa-B essential modulator


Theoretical massNumber of molelcules
Total (without water)13,5682
Polymers13,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
MethodPISA
4
A: Inhibitor of nuclear factor kappa-B kinase subunit beta,Inhibitor of nuclear factor kappa-B kinase subunit alpha
D: NF-kappa-B essential modulator


Theoretical massNumber of molelcules
Total (without water)13,5682
Polymers13,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
MethodPISA
5
B: NF-kappa-B essential modulator
C: Inhibitor of nuclear factor kappa-B kinase subunit beta,Inhibitor of nuclear factor kappa-B kinase subunit alpha


Theoretical massNumber of molelcules
Total (without water)13,5682
Polymers13,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.869, 105.556, 56.707
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,Inhibitor of nuclear factor kappa-B kinase subunit alpha / 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 / I kappa-B kinase alpha / IkBKA / IKK-alpha / IKK-A / IkappaB kinase / I-kappa-B kinase 1 / IKK1 / Conserved helix-loop-helix / ubiquitous kinase / Nuclear factor NF-kappa-B / inhibitor kinase alpha / NFKBIKA /


Mass: 5293.937 Da / Num. of mol.: 2
Fragment: Fusion protein consists of UNP residues 701-730 of IKK-B and nemo-binding domain of IKK-A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IKBKB, IKKB / Plasmid: pet11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O14920, UniProt: O15111, 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: 8274.388 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IKBKG, FIP3, NEMO / References: UniProt: Q9Y6K9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 298 K / Method: microbatch under oil / pH: 8
Details: 35% Peg 8K, 0.1M Tris pH 8, 0.2M Ammonium Chloride, 10mM Dithiothreitol., microbatch under oil, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9794,0.9799
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2005 / Details: Undulator, mirrors
RadiationMonochromator: Graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97991
ReflectionResolution: 2.25→38.9 Å / Num. all: 12598 / Num. obs: 11760 / % possible obs: 93.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Biso Wilson estimate: 70.6 Å2 / Rmerge(I) obs: 0.072
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 1.7 / Num. unique all: 849 / % possible all: 69.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→38.9 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU B: 17.198 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28186 556 4.8 %RANDOM
Rwork0.23756 ---
obs0.23961 11119 93.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.296 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20 Å2
2--1.01 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.25→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1599 0 0 62 1661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0211610
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.9592170
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3175203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.44424.69983
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.63615289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6771515
X-RAY DIFFRACTIONr_chiral_restr0.1390.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021221
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.240.2695
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.21098
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2730.252
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.280.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2451.51059
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.02821601
X-RAY DIFFRACTIONr_scbond_it2.8553626
X-RAY DIFFRACTIONr_scangle_it4.444.5568
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 32 -
Rwork0.257 587 -
obs--68.25 %

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