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- PDB-1ikn: IKAPPABALPHA/NF-KAPPAB COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1ikn
TitleIKAPPABALPHA/NF-KAPPAB COMPLEX
Components
  • PROTEIN (I-KAPPA-B-ALPHA)
  • PROTEIN (NF-KAPPA-B P50D SUBUNIT)
  • PROTEIN (NF-KAPPA-B P65 SUBUNIT)
KeywordsTRANSCRIPTION FACTOR / IKB-NFKB COMPLEX
Function / homology
Function and homology information


I-kappaB/NF-kappaB complex / cellular response to diterpene / cellular response to glucoside / SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TRAF6 mediated NF-kB activation ...I-kappaB/NF-kappaB complex / cellular response to diterpene / cellular response to glucoside / SUMOylation of immune response proteins / Regulated proteolysis of p75NTR / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TRAF6 mediated NF-kB activation / cytoplasmic sequestering of NF-kappaB / positive regulation of hyaluronan biosynthetic process / NF-kB is activated and signals survival / antibacterial innate immune response / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / cellular response to carbohydrate stimulus / negative regulation of myeloid cell differentiation / mammary gland involution / FCERI mediated NF-kB activation / positive regulation of chondrocyte differentiation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / cellular response to peptide / acetaldehyde metabolic process / cellular response to interleukin-17 / Downstream TCR signaling / prolactin signaling pathway / NF-kappaB p50/p65 complex / nucleotide-binding oligomerization domain containing 1 signaling pathway / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / molecular sequestering activity / CD209 (DC-SIGN) signaling / cellular response to peptidoglycan / negative regulation of interleukin-12 production / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / negative regulation of protein sumoylation / cellular response to dsRNA / nucleotide-binding oligomerization domain containing 2 signaling pathway / postsynapse to nucleus signaling pathway / defense response to tumor cell / cellular response to interleukin-6 / transcription regulator inhibitor activity / actinin binding / NF-kappaB complex / negative regulation of non-canonical NF-kappaB signal transduction / cellular response to angiotensin / response to UV-B / interleukin-1-mediated signaling pathway / vascular endothelial growth factor signaling pathway / negative regulation of cytokine production / toll-like receptor 4 signaling pathway / cellular response to cold / positive regulation of leukocyte adhesion to vascular endothelial cell / nuclear localization sequence binding / positive regulation of miRNA metabolic process / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / response to exogenous dsRNA / positive regulation of T cell receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / response to cobalamin / negative regulation of Notch signaling pathway / phosphate ion binding / cellular response to cytokine stimulus / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation / cellular response to lipoteichoic acid / response to muramyl dipeptide / positive regulation of cholesterol efflux / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / general transcription initiation factor binding / cellular response to organic cyclic compound / NF-kappaB binding / hair follicle development / neuropeptide signaling pathway / positive regulation of vascular endothelial growth factor production / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / lymph node development / response to amino acid / canonical NF-kappaB signal transduction / cellular response to interleukin-1 / negative regulation of canonical NF-kappaB signal transduction / JNK cascade / Notch signaling pathway / cellular response to brain-derived neurotrophic factor stimulus / lipopolysaccharide-mediated signaling pathway / negative regulation of insulin receptor signaling pathway / response to cAMP / tumor necrosis factor-mediated signaling pathway / heat shock protein binding / response to muscle stretch / positive regulation of protein metabolic process / NF-kB is activated and signals survival
Similarity search - Function
Ankyrin repeats (many copies) / Rel homology domain (RHD), DNA-binding domain / : / Nuclear factor NF-kappa-B, p105 subunit / Transcription factor RelA (p65) / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain ...Ankyrin repeats (many copies) / Rel homology domain (RHD), DNA-binding domain / : / Nuclear factor NF-kappa-B, p105 subunit / Transcription factor RelA (p65) / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Ankyrin repeat-containing domain / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Nuclear factor NF-kappa-B p105 subunit / NF-kappa-B inhibitor alpha / Transcription factor p65
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHuxford, T. / Huang, D.-B. / Malek, S. / Ghosh, G.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: The crystal structure of the IkappaBalpha/NF-kappaB complex reveals mechanisms of NF-kappaB inactivation.
Authors: Huxford, T. / Huang, D.B. / Malek, S. / Ghosh, G.
History
DepositionNov 13, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (NF-KAPPA-B P65 SUBUNIT)
C: PROTEIN (NF-KAPPA-B P50D SUBUNIT)
D: PROTEIN (I-KAPPA-B-ALPHA)


Theoretical massNumber of molelcules
Total (without water)72,7663
Polymers72,7663
Non-polymers00
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-15 kcal/mol
Surface area28830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.500, 49.300, 120.600
Angle α, β, γ (deg.)90.00, 108.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN (NF-KAPPA-B P65 SUBUNIT) / P65


Mass: 32738.027 Da / Num. of mol.: 1 / Fragment: N-TERMINAL AND DIMERIZATION DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q04207
#2: Protein PROTEIN (NF-KAPPA-B P50D SUBUNIT) / P50D


Mass: 13929.799 Da / Num. of mol.: 1 / Fragment: N-TERMINAL AND DIMERIZATION DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P25799
#3: Protein PROTEIN (I-KAPPA-B-ALPHA)


Mass: 26098.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAD-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P25963
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 43 %
Crystal growpH: 7 / Details: pH 7.00
Crystal
*PLUS
Density % sol: 43 %
Crystal grow
*PLUS
Temperature: 23-24 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
225 mMMES1drop
36.5 %PEG80001drop
42.5 mMdithiothreitol1drop
550 mMMES1reservoir
610 %PEG80001reservoir
75 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.54
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 28014 / % possible obs: 91 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 15.1
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.5 / % possible all: 59
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / % possible obs: 91 % / Redundancy: 3.5 % / Num. measured all: 160828
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.38 Å / % possible obs: 59 % / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VKX

1vkx


Resolution: 2.3→6 Å / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1105 5 %RANDOM
Rwork0.223 ---
obs-21795 74.2 %-
Displacement parametersBiso mean: 48.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å26.29 Å2
2---4.96 Å20 Å2
3---4.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-6 Å
Luzzati sigma a0.47 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4767 0 0 212 4979
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
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
LS refinement shellResolution: 2.3→2.44 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 97 5.6 %
Rwork0.3 1634 -
obs--35.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95
LS refinement shell
*PLUS
Rfactor obs: 0.3

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