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- PDB-2i9t: Structure of NF-kB p65-p50 heterodimer bound to PRDII element of ... -

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Basic information

Entry
Database: PDB / ID: 2i9t
TitleStructure of NF-kB p65-p50 heterodimer bound to PRDII element of B-interferon promoter
Components
  • 5'-D(*AP*GP*TP*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*CP*TP*G)-3'
  • 5'-D(*CP*AP*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*CP*AP*CP*T)-3'
  • Nuclear factor NF-kappa-B p105 subunit
  • Transcription factor p65
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


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 / positive regulation of hyaluronan biosynthetic process ...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 / positive regulation of hyaluronan biosynthetic process / NF-kB is activated and signals survival / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / antibacterial innate immune response / TAK1-dependent IKK and NF-kappa-B activation / cellular response to carbohydrate stimulus / mammary gland involution / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / positive regulation of chondrocyte differentiation / Interleukin-1 signaling / cellular response to peptide / acetaldehyde metabolic process / Downstream TCR signaling / prolactin signaling pathway / cellular response to interleukin-17 / NF-kappaB p50/p65 complex / positive regulation of Schwann cell differentiation / CD209 (DC-SIGN) signaling / cellular response to peptidoglycan / negative regulation of interleukin-12 production / ankyrin repeat binding / negative regulation of protein sumoylation / defense response to tumor cell / cellular response to dsRNA / postsynapse to nucleus signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to interleukin-6 / actinin binding / cellular response to angiotensin / response to UV-B / NF-kappaB complex / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of leukocyte adhesion to vascular endothelial cell / 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 hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / positive regulation of miRNA metabolic process / response to cobalamin / positive regulation of T cell receptor signaling pathway / non-canonical NF-kappaB signal transduction / phosphate ion binding / cellular response to cytokine stimulus / cellular response to lipoteichoic acid / response to muramyl dipeptide / cellular response to organic cyclic compound / general transcription initiation factor binding / NF-kappaB binding / hair follicle development / positive regulation of vascular endothelial growth factor production / positive regulation of transcription initiation by RNA polymerase II / neuropeptide signaling pathway / canonical NF-kappaB signal transduction / RNA polymerase II core promoter sequence-specific DNA binding / response to amino acid / cellular response to interleukin-1 / lymph node development / JNK cascade / cellular response to brain-derived neurotrophic factor stimulus / response to cAMP / tumor necrosis factor-mediated signaling pathway / heat shock protein binding / response to muscle stretch / positive regulation of interleukin-12 production / negative regulation of insulin receptor signaling pathway / Neutrophil degranulation / negative regulation of angiogenesis / negative regulation of miRNA transcription / liver development / positive regulation of interleukin-1 beta production / response to cytokine / positive regulation of interleukin-8 production / response to ischemia / response to progesterone / negative regulation of extrinsic apoptotic signaling pathway / transcription coregulator activity / animal organ morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / response to bacterium / B cell receptor signaling pathway / protein catabolic process / response to insulin / negative regulation of protein catabolic process / response to organic cyclic compound / chromatin DNA binding / cellular response to virus
Similarity search - Function
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 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 / 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 / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear factor NF-kappa-B p105 subunit / Transcription factor p65
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsEscalante, C.R. / Shen, L. / Thanos, D. / Aggarwal, A.K.
CitationJournal: Structure / Year: 2002
Title: Structure of NF-kappaB p50/p65 heterodimer bound to the PRDII DNA element from the interferon-beta promoter
Authors: Escalante, C.R. / Shen, L. / Thanos, D. / Aggarwal, A.K.
History
DepositionSep 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 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

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*AP*GP*TP*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*CP*TP*G)-3'
D: 5'-D(*CP*AP*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*CP*AP*CP*T)-3'
A: Transcription factor p65
B: Nuclear factor NF-kappa-B p105 subunit


Theoretical massNumber of molelcules
Total (without water)77,1034
Polymers77,1034
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.620, 166.110, 60.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: DNA chain 5'-D(*AP*GP*TP*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*CP*TP*G)-3'


Mass: 5242.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PRDII DNA element
#2: DNA chain 5'-D(*CP*AP*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*CP*AP*CP*T)-3'


Mass: 5171.374 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Transcription factor p65 / Nuclear factor NF-kappa-B p65 subunit


Mass: 31632.771 Da / Num. of mol.: 1 / Fragment: residues 19-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rela, Nfkb3 / Plasmid: PET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q04207
#4: Protein Nuclear factor NF-kappa-B p105 subunit


Mass: 35056.066 Da / Num. of mol.: 1 / Fragment: residues 39-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nfkb1 / Plasmid: PET-9a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25799
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.16 Å3/Da / Density % sol: 61.09 %
Crystal growTemperature: 293 K / pH: 5.6
Details: 8% PEG 5K monomethylether, 200mM sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.60
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium acetate11
2PEG 5K monomethylether11
3HOH11
4sodium acetate12
5PEG 5K monomethylether12
6HOH12

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Feb 8, 1999
RadiationMonochromator: PT-COATED TOROIDAL SI MIRROR FOR HORIZONTAL AND VERTICAL FOCUSSING FOLLOWED BY DOUBLE FLAT SI CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 24691 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.68 % / Biso Wilson estimate: 74.2 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 27.87
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.337 / % possible all: 96.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→34.46 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.288 2438 -RANDOM
Rwork0.233 ---
obs0.233 24647 99.3 %-
Displacement parametersBiso mean: 52.3 Å2
Baniso -1Baniso -2Baniso -3
1--8 Å20 Å20 Å2
2--4.66 Å20 Å2
3---3.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.8→34.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4514 691 0 21 5226
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_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.34
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

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