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- PDB-9bdw: NF-kappaB RelA homo-dimer bound to GC-centric kappaB DNA -

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Basic information

Entry
Database: PDB / ID: 9bdw
TitleNF-kappaB RelA homo-dimer bound to GC-centric kappaB DNA
Components
  • DNA (5'-D(P*AP*CP*TP*GP*GP*GP*AP*AP*GP*TP*TP*CP*CP*AP*GP*TP*GP*AP*T)-3')
  • DNA (5'-D(P*AP*TP*CP*AP*CP*TP*GP*GP*AP*AP*CP*TP*TP*CP*CP*CP*AP*GP*T)-3')
  • Transcription factor p65
KeywordsDNA BINDING PROTEIN/DNA / RelA / kappaB DNA / Promoter / Transcription / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


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 / TRAF6 mediated NF-kB activation / 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 ...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 / TRAF6 mediated NF-kB activation / 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 / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / Downstream TCR signaling / prolactin signaling pathway / NF-kappaB p50/p65 complex / toll-like receptor TLR6:TLR2 signaling pathway / positive regulation of Schwann cell differentiation / CD209 (DC-SIGN) signaling / cellular response to peptidoglycan / ankyrin repeat binding / postsynapse to nucleus signaling pathway / negative regulation of protein sumoylation / defense response to tumor cell / cellular response to interleukin-6 / nucleotide-binding oligomerization domain containing 2 signaling pathway / actinin binding / response to UV-B / negative regulation of non-canonical NF-kappaB signal transduction / non-canonical NF-kappaB signal transduction / positive regulation of leukocyte adhesion to vascular endothelial cell / interleukin-1-mediated signaling pathway / NF-kappaB complex / vascular endothelial growth factor signaling pathway / toll-like receptor 4 signaling pathway / positive regulation of amyloid-beta formation / cellular response to hepatocyte growth factor stimulus / response to cobalamin / phosphate ion binding / positive regulation of T cell receptor signaling pathway / cellular response to lipoteichoic acid / response to muramyl dipeptide / general transcription initiation factor binding / cellular response to angiotensin / positive regulation of vascular endothelial growth factor production / canonical NF-kappaB signal transduction / hair follicle development / response to amino acid / neuropeptide signaling pathway / NF-kappaB binding / RNA polymerase II core promoter sequence-specific DNA binding / response to cAMP / tumor necrosis factor-mediated signaling pathway / response to muscle stretch / antiviral innate immune response / positive regulation of interleukin-12 production / negative regulation of insulin receptor signaling pathway / negative regulation of miRNA transcription / peptide binding / negative regulation of angiogenesis / liver development / response to progesterone / positive regulation of interleukin-1 beta production / response to ischemia / animal organ morphogenesis / positive regulation of interleukin-8 production / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of extrinsic apoptotic signaling pathway / response to insulin / response to bacterium / protein catabolic process / defense response / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of protein catabolic process / chromatin DNA binding / positive regulation of miRNA transcription / positive regulation of interleukin-6 production / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to nicotine / cellular response to hydrogen peroxide / histone deacetylase binding / positive regulation of NF-kappaB transcription factor activity / cellular response to tumor necrosis factor / chromatin organization / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of inflammatory response / transcription regulator complex / sequence-specific DNA binding / response to ethanol / positive regulation of canonical NF-kappaB signal transduction / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / DNA-templated transcription / positive regulation of cell population proliferation / ubiquitin protein ligase binding
Similarity search - Function
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. ...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 / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor p65
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsBiswas, T. / Shahabi, S. / Tsodikov, O.V. / Huang, D. / Ghosh, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM085490-11 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Transient interactions modulate the affinity of NF-kappa B transcription factors for DNA.
Authors: Li, T. / Shahabi, S. / Biswas, T. / Tsodikov, O.V. / Pan, W. / Huang, D.B. / Wang, V.Y. / Wang, Y. / Ghosh, G.
History
DepositionApr 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor p65
B: Transcription factor p65
C: DNA (5'-D(P*AP*CP*TP*GP*GP*GP*AP*AP*GP*TP*TP*CP*CP*AP*GP*TP*GP*AP*T)-3')
D: DNA (5'-D(P*AP*TP*CP*AP*CP*TP*GP*GP*AP*AP*CP*TP*TP*CP*CP*CP*AP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,16110
Polymers77,3884
Non-polymers7736
Water10,160564
1
B: Transcription factor p65
C: DNA (5'-D(P*AP*CP*TP*GP*GP*GP*AP*AP*GP*TP*TP*CP*CP*AP*GP*TP*GP*AP*T)-3')
D: DNA (5'-D(P*AP*TP*CP*AP*CP*TP*GP*GP*AP*AP*CP*TP*TP*CP*CP*CP*AP*GP*T)-3')
hetero molecules

A: Transcription factor p65
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,16110
Polymers77,3884
Non-polymers7736
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area6000 Å2
ΔGint-127 kcal/mol
Surface area34470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.263, 133.084, 45.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(P*AP*CP*TP*GP*GP*GP*AP*AP*GP*TP*TP*CP*CP*AP*GP*TP*GP*AP*T)-3')


Mass: 5884.821 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*AP*TP*CP*AP*CP*TP*GP*GP*AP*AP*CP*TP*TP*CP*CP*CP*AP*GP*T)-3')


Mass: 5764.749 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Transcription factor p65 / Nuclear factor NF-kappa-B p65 subunit / Nuclear factor of kappa light polypeptide gene enhancer in B-cells 3


Mass: 32869.223 Da / Num. of mol.: 2 / Fragment: residues 19-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rela, Nfkb3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04207
#5: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 2 types, 569 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, MES, Spermine, beta-octylglucoside

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.87→30 Å / Num. obs: 60489 / % possible obs: 99.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.987 / Χ2: 0.082 / Net I/σ(I): 9.6 / Num. measured all: 409360
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.87-1.95.83.69630190.903199.8
1.9-1.945.92.81629400.882199.9
1.94-1.976.22.03229980.939199.9
1.97-2.016.41.53829960.958199.9
2.01-2.066.61.29430040.991100
2.06-2.116.81.12129771.0171100
2.11-2.166.91.01830291.0161100
2.16-2.227.11.01929830.9841100
2.22-2.287.10.83730330.9471100
2.28-2.367.10.65529910.9521100
2.36-2.447.10.49330200.9561100
2.44-2.547.10.35730440.9511100
2.54-2.657.10.24830150.9391100
2.65-2.797.10.17630160.9611100
2.79-2.977.20.12530590.9861100
2.97-3.27.20.09230441.0971100
3.2-3.527.20.07330921.2461100
3.52-4.0370.0630751.103199.9
4.03-5.076.50.04631070.783199.1
5.07-3060.04730470.73192.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RAM

2ram


Resolution: 1.87→29.82 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.356 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.332 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22729 2947 5 %RANDOM
Rwork0.15364 ---
obs0.15729 56382 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.033 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0 Å2
2---0.01 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.87→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4373 781 45 564 5763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125398
X-RAY DIFFRACTIONr_bond_other_d0.0110.0164444
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.6937488
X-RAY DIFFRACTIONr_angle_other_deg0.5671.56110455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6025549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.604549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.31310748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.2811
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025673
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02994
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.822.4562202
X-RAY DIFFRACTIONr_mcbond_other3.8212.4562202
X-RAY DIFFRACTIONr_mcangle_it4.6983.6572749
X-RAY DIFFRACTIONr_mcangle_other4.7083.662750
X-RAY DIFFRACTIONr_scbond_it6.8773.83196
X-RAY DIFFRACTIONr_scbond_other6.863.7833189
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.1035.5484728
X-RAY DIFFRACTIONr_long_range_B_refined9.38649.6966277
X-RAY DIFFRACTIONr_long_range_B_other9.42747.5286146
X-RAY DIFFRACTIONr_rigid_bond_restr4.30439806
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.87→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 161 -
Rwork0.209 3103 -
obs--73.4 %

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