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- PDB-1nfi: I-KAPPA-B-ALPHA/NF-KAPPA-B COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1nfi
TitleI-KAPPA-B-ALPHA/NF-KAPPA-B COMPLEX
Components
  • I-KAPPA-B-ALPHA
  • NF-KAPPA-B P50
  • NF-KAPPA-B P65
KeywordsCOMPLEX (TRANSCRIPTION REG/ANK REPEAT) / COMPLEX (TRANSCRIPTION REGULATION-ANK REPEAT) / ANKYRIN REPEAT / COMPLEX (TRANSCRIPTION REG-ANK REPEAT) COMPLEX
Function / homology
Function and homology information


negative regulation of calcidiol 1-monooxygenase activity / negative regulation of vitamin D biosynthetic process / I-kappaB/NF-kappaB complex / negative regulation of cholesterol transport / cytoplasmic sequestering of NF-kappaB / positive regulation of hyaluronan biosynthetic process / antibacterial innate immune response / negative regulation of myeloid cell differentiation / mammary gland involution / acetaldehyde metabolic process ...negative regulation of calcidiol 1-monooxygenase activity / negative regulation of vitamin D biosynthetic process / I-kappaB/NF-kappaB complex / negative regulation of cholesterol transport / cytoplasmic sequestering of NF-kappaB / positive regulation of hyaluronan biosynthetic process / antibacterial innate immune response / negative regulation of myeloid cell differentiation / mammary gland involution / acetaldehyde metabolic process / cellular response to interleukin-17 / prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / nucleotide-binding oligomerization domain containing 1 signaling pathway / IkBA variant leads to EDA-ID / positive regulation of macrophage derived foam cell differentiation / positive regulation of Schwann cell differentiation / positive regulation of lipid storage / molecular sequestering activity / cellular response to peptidoglycan / Regulated proteolysis of p75NTR / negative regulation of interleukin-12 production / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / CLEC7A/inflammasome pathway / negative regulation of protein sumoylation / cellular response to dsRNA / postsynapse to nucleus signaling pathway / defense response to tumor cell / nucleotide-binding oligomerization domain containing 2 signaling pathway / Interleukin-1 processing / cellular response to interleukin-6 / actinin binding / negative regulation of non-canonical NF-kappaB signal transduction / NF-kappaB complex / cellular response to angiotensin / transcription regulator inhibitor activity / response to UV-B / vascular endothelial growth factor signaling pathway / interleukin-1-mediated signaling pathway / Regulation of NFE2L2 gene expression / cellular response to cold / positive regulation of leukocyte adhesion to vascular endothelial cell / negative regulation of protein metabolic process / positive regulation of miRNA metabolic process / toll-like receptor 4 signaling pathway / nuclear localization sequence binding / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / 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 / response to exogenous dsRNA / phosphate ion binding / non-canonical NF-kappaB signal transduction / cellular response to lipoteichoic acid / TRAF6 mediated NF-kB activation / response to muramyl dipeptide / negative regulation of macrophage derived foam cell differentiation / The NLRP3 inflammasome / negative regulation of lipid storage / general transcription initiation factor binding / Transcriptional Regulation by VENTX / NF-kappaB binding / hair follicle development / neuropeptide signaling pathway / positive regulation of transcription initiation by RNA polymerase II / positive regulation of vascular endothelial growth factor production / positive regulation of cholesterol efflux / RNA polymerase II core promoter sequence-specific DNA binding / canonical NF-kappaB signal transduction / response to amino acid / cellular response to interleukin-1 / cellular defense response / Purinergic signaling in leishmaniasis infection / negative regulation of canonical NF-kappaB signal transduction / JNK cascade / Notch signaling pathway / lipopolysaccharide-mediated signaling pathway / negative regulation of insulin receptor signaling pathway / response to cAMP / tumor necrosis factor-mediated signaling pathway / response to muscle stretch / positive regulation of protein metabolic process / positive regulation of interleukin-12 production / NF-kB is activated and signals survival / CD209 (DC-SIGN) signaling / response to interleukin-1 / negative regulation of angiogenesis / MAP3K8 (TPL2)-dependent MAPK1/3 activation / protein sequestering activity / negative regulation of miRNA transcription / liver development / response to progesterone / response to organic substance / positive regulation of interleukin-1 beta production / response to cytokine
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.7 Å
AuthorsJacobs, M.D. / Harrison, S.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Structure of an IkappaBalpha/NF-kappaB complex.
Authors: Jacobs, M.D. / Harrison, S.C.
History
DepositionAug 25, 1998Processing site: BNL
Revision 1.0Nov 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: NF-KAPPA-B P65
B: NF-KAPPA-B P50
C: NF-KAPPA-B P65
D: NF-KAPPA-B P50
E: I-KAPPA-B-ALPHA
F: I-KAPPA-B-ALPHA


Theoretical massNumber of molelcules
Total (without water)140,6046
Polymers140,6046
Non-polymers00
Water1,27971
1
A: NF-KAPPA-B P65
B: NF-KAPPA-B P50
F: I-KAPPA-B-ALPHA


Theoretical massNumber of molelcules
Total (without water)70,3023
Polymers70,3023
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-17 kcal/mol
Surface area28880 Å2
MethodPISA
2
C: NF-KAPPA-B P65
D: NF-KAPPA-B P50
E: I-KAPPA-B-ALPHA


Theoretical massNumber of molelcules
Total (without water)70,3023
Polymers70,3023
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-21 kcal/mol
Surface area29210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.094, 91.080, 190.980
Angle α, β, γ (deg.)90.00, 96.32, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, 0.003, -0.001), (-0.003, -1, -0.004), (-0.001, -0.004, 1)
Vector: -10.255, 131.397, -94.817)

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Components

#1: Protein NF-KAPPA-B P65


Mass: 34547.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q04206
#2: Protein NF-KAPPA-B P50


Mass: 12442.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P19838
#3: Protein I-KAPPA-B-ALPHA


Mass: 23312.512 Da / Num. of mol.: 2 / Fragment: ANKYRIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P25963
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.02 Å3/Da / Density % sol: 59 %
Crystal growpH: 5 / Details: pH 5.0
Crystal grow
*PLUS
Temperature: 4, 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
275 mMammonium acetate1drop
310 mMdithiothreitol1drop
41 mMethylenediamine tetraacetic acid1drop
50.05 %n-octyl-beta-D-glucopyranoside1drop
68 mMTris-HCl1drop
725 mMsodium acetate1reservoir
88-10 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9879
DetectorType: BRANDEIS - B4 / Detector: CCD
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9879 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 41990 / % possible obs: 92 % / Redundancy: 3.6 % / Biso Wilson estimate: 60.4 Å2 / Rsym value: 0.05
Reflection
*PLUS
Redundancy: 3.7 % / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 83 % / Rmerge(I) obs: 0.206

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.5phasing
RefinementMethod to determine structure: MIR / Resolution: 2.7→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 1441954.76 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2093 5 %SHELLS
Rwork0.223 ---
obs0.223 41835 90.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.18 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso mean: 59.8 Å2
Baniso -1Baniso -2Baniso -3
1--7.18 Å20 Å24.41 Å2
2---7.09 Å20 Å2
3---14.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9831 0 0 71 9902
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.251.5
X-RAY DIFFRACTIONc_mcangle_it4.972
X-RAY DIFFRACTIONc_scbond_it5.492
X-RAY DIFFRACTIONc_scangle_it6.732.5
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.374 183 4.9 %
Rwork0.316 3541 -
obs--81.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 39742 / Rfactor obs: 0.222 / Rfactor Rfree: 0.315
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
Rfactor obs: 0.315

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