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

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Basic information

Entry
Database: PDB / ID: 8tkl
TitleMurine NF-kappaB p50 Rel Homology Region homodimer in complex with a Test 16-mer kappaB-like DNA
Components
  • (Test 17-mer kappaB-like 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 / negative regulation of vitamin D biosynthetic process / 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 ...Regulated proteolysis of p75NTR / I-kappaB/NF-kappaB complex / negative regulation of vitamin D biosynthetic process / 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 / mammary gland involution / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / 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 / positive regulation of macrophage derived foam cell differentiation / cellular response to dsRNA / actinin binding / non-canonical NF-kappaB signal transduction / positive regulation of miRNA metabolic process / signal transduction involved in regulation of gene expression / negative regulation of cytokine production / cellular response to cytokine stimulus / cellular response to angiotensin / canonical NF-kappaB signal transduction / positive regulation of cholesterol efflux / positive regulation of transcription initiation by RNA polymerase II / lymph node development / JNK cascade / response to muscle stretch / Neutrophil degranulation / negative regulation of cytokine production involved in inflammatory response / B cell receptor signaling pathway / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cellular response to mechanical stimulus / cellular response to virus / cellular response to nicotine / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to tumor necrosis factor / positive regulation of canonical Wnt signaling pathway / MAPK cascade / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / gene expression / 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 / cytoplasm / cytosol
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: 3 Å
AuthorsMitchel, S. / Mealka, M. / Rogers, W.E. / Milani, C. / Acuna, L.M. / 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 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,2654
Polymers80,2654
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.152, 146.452, 67.688
Angle α, β, γ (deg.)90.000, 98.620, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 39 - 350 / Label seq-ID: 1 - 312

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.537121976916, -0.698434000325, 0.472958697039), (-0.705953339578, 0.0653384015666, -0.705238098531), (0.461659901067, -0.712685653336, -0.528156506422)Vector: 48. ...NCS oper: (Code: given
Matrix: (-0.537121976916, -0.698434000325, 0.472958697039), (-0.705953339578, 0.0653384015666, -0.705238098531), (0.461659901067, -0.712685653336, -0.528156506422)
Vector: 48.2039925826, 0.205511376507, -47.2122094702)

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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 Test 17-mer kappaB-like DNA


Mass: 5163.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain Test 17-mer kappaB-like DNA


Mass: 5252.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has protein modificationY

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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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 4% Tacsimate pH 6.0, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→146.45 Å / Num. obs: 17962 / % possible obs: 98.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 76.35 Å2 / Rsym value: 0.094 / Net I/σ(I): 10.1
Reflection shellResolution: 3→3.16 Å / Rmerge(I) obs: 0.035 / Num. unique obs: 1805 / Rsym value: 0.631

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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 / Resolution: 3→73.23 Å / SU ML: 0.4687 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 31.3187
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2843 915 5.1 %
Rwork0.2247 17018 -
obs0.2276 17933 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.13 Å2
Refinement stepCycle: LAST / Resolution: 3→73.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4906 691 0 0 5597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00255784
X-RAY DIFFRACTIONf_angle_d0.58397959
X-RAY DIFFRACTIONf_chiral_restr0.0421874
X-RAY DIFFRACTIONf_plane_restr0.0047920
X-RAY DIFFRACTIONf_dihedral_angle_d16.91552228
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.84619081273 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.160.37611450.32342455X-RAY DIFFRACTION98.97
3.16-3.360.35431260.28482401X-RAY DIFFRACTION97.57
3.36-3.620.40931150.28212441X-RAY DIFFRACTION98.99
3.62-3.980.32861310.24692426X-RAY DIFFRACTION98.69
3.98-4.550.2521160.22052418X-RAY DIFFRACTION97.84
4.56-5.740.26551340.19872436X-RAY DIFFRACTION99
5.74-73.230.22221480.18122441X-RAY DIFFRACTION97.92

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