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- PDB-8tkm: Murine NF-kappaB p50 Rel Homology Region homodimer in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8tkm
TitleMurine NF-kappaB p50 Rel Homology Region homodimer in complex with 17-mer kappaB DNA from human interleukin-6 (IL-6) promoter
Components
  • (17-mer kappaB DNA) x 2
  • Nuclear factor NF-kappa-B p50 subunit
KeywordsTRANSCRIPTION/DNA / DNA / NF-kappaB / p50 / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


Regulated proteolysis of p75NTR / I-kappaB/NF-kappaB complex / 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 ...Regulated proteolysis of p75NTR / I-kappaB/NF-kappaB complex / 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 / TAK1-dependent IKK and NF-kappa-B activation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / mammary gland involution / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / antibacterial innate immune response / Downstream TCR signaling / cellular response to interleukin-17 / NF-kappaB p50/p65 complex / CD209 (DC-SIGN) signaling / positive regulation of lipid storage / negative regulation of interleukin-12 production / cellular response to interleukin-6 / cellular response to dsRNA / actinin binding / positive regulation of macrophage derived foam cell differentiation / non-canonical NF-kappaB signal transduction / positive regulation of miRNA metabolic process / negative regulation of cytokine production / cellular response to cytokine stimulus / : / cellular response to interleukin-1 / cellular response to angiotensin / positive regulation of cholesterol efflux / canonical NF-kappaB signal transduction / positive regulation of transcription initiation by RNA polymerase II / lymph node development / JNK cascade / response to muscle stretch / Neutrophil degranulation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / B cell receptor signaling pathway / transcription coregulator activity / cellular response to virus / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to nicotine / negative regulation of inflammatory response / cellular response to mechanical stimulus / positive regulation of canonical Wnt signaling pathway / MAPK cascade / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / gene expression / transcription regulator complex / sequence-specific DNA binding / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / apoptotic process / chromatin binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear factor NF-kappa-B, p105 subunit / : / 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 ...Nuclear factor NF-kappa-B, p105 subunit / : / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear factor NF-kappa-B p105 subunit
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhu, N. / Mealka, M. / Mitchel, S. / Rogers, W.E. / Huxford, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biomolecules / Year: 2023
Title: X-ray Crystallographic Study of Preferred Spacing by the NF-kappa B p50 Homodimer on kappa B DNA.
Authors: Zhu, N. / Mealka, M. / Mitchel, S. / Milani, C. / Acuna, L.M. / Rogers, E. / Lahana, A.N. / Huxford, T.
History
DepositionJul 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear factor NF-kappa-B p50 subunit
B: Nuclear factor NF-kappa-B p50 subunit
C: 17-mer kappaB DNA
D: 17-mer kappaB DNA


Theoretical massNumber of molelcules
Total (without water)80,2644
Polymers80,2644
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.172, 162.172, 60.384
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Nuclear factor NF-kappa-B p50 subunit


Mass: 34924.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nfkb1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25799
#2: DNA chain 17-mer kappaB DNA


Mass: 5224.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain 17-mer kappaB DNA


Mass: 5189.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Na-Acetate pH 4.9, 16% (w/v) PEG 1500 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→48.43 Å / Num. obs: 22616 / % possible obs: 99.9 % / Redundancy: 17.5 % / Biso Wilson estimate: 59.41 Å2 / Rsym value: 0.079 / Net I/σ(I): 17.9
Reflection shellResolution: 2.8→2.92 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 2260 / Rsym value: 0.594

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Processing

Software
NameVersionClassification
HKL-2000data collection
autoPROCdata processing
PHENIX1.20.1_4487model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NFK

1nfk


Resolution: 2.8→48.43 Å / SU ML: 0.4339 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.81
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2726 1155 5.12 %
Rwork0.2248 21412 -
obs0.2272 22567 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.27 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4903 690 0 55 5648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00295780
X-RAY DIFFRACTIONf_angle_d0.61587953
X-RAY DIFFRACTIONf_chiral_restr0.0428873
X-RAY DIFFRACTIONf_plane_restr0.0047920
X-RAY DIFFRACTIONf_dihedral_angle_d18.27342226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.930.40581510.37542640X-RAY DIFFRACTION99.18
2.93-3.080.39381240.30342649X-RAY DIFFRACTION99.68
3.08-3.270.34671460.25732654X-RAY DIFFRACTION99.54
3.27-3.530.35651570.26572663X-RAY DIFFRACTION99.89
3.53-3.880.24791620.21972639X-RAY DIFFRACTION99.72
3.88-4.440.25061430.20692663X-RAY DIFFRACTION100
4.44-5.590.22211350.19062727X-RAY DIFFRACTION99.79
5.6-48.430.21411370.18922777X-RAY DIFFRACTION99.83

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