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- PDB-9e6w: NF-kappaB RelA homo-dimer bound to a kappaB site of Cxcl2 gene -

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Basic information

Entry
Database: PDB / ID: 9e6w
TitleNF-kappaB RelA homo-dimer bound to a kappaB site of Cxcl2 gene
Components
  • DNA (5'-D(P*AP*CP*TP*GP*GP*GP*CP*TP*TP*TP*TP*CP*CP*AP*GP*TP*GP*A)-3')
  • DNA (5'-D(P*TP*CP*AP*CP*TP*GP*GP*AP*AP*AP*AP*GP*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 / response to cobalamin / CD209 (DC-SIGN) signaling / cellular response to peptidoglycan / ankyrin repeat binding / negative regulation of protein sumoylation / postsynapse to nucleus signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / defense response to tumor cell / cellular response to interleukin-6 / actinin binding / response to UV-B / non-canonical NF-kappaB signal transduction / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of leukocyte adhesion to vascular endothelial cell / interleukin-1-mediated signaling pathway / NF-kappaB complex / signal transduction involved in regulation of gene expression / vascular endothelial growth factor signaling pathway / toll-like receptor 4 signaling pathway / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / phosphate ion binding / positive regulation of T cell receptor signaling pathway / cellular response to lipoteichoic acid / response to muramyl dipeptide / positive regulation of vascular endothelial growth factor production / cellular response to angiotensin / general transcription initiation factor binding / response to cAMP / canonical NF-kappaB signal transduction / hair follicle development / neuropeptide signaling pathway / NF-kappaB binding / response to amino acid / RNA polymerase II core promoter sequence-specific DNA binding / response to muscle stretch / positive regulation of interleukin-12 production / antiviral innate immune response / negative regulation of cytokine production involved in inflammatory response / peptide binding / negative regulation of insulin receptor signaling pathway / response to progesterone / negative regulation of miRNA transcription / negative regulation of angiogenesis / animal organ morphogenesis / response to ischemia / positive regulation of interleukin-1 beta production / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / response to bacterium / protein catabolic process / liver development / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / defense response / response to insulin / negative regulation of protein catabolic process / chromatin DNA binding / positive regulation of interleukin-6 production / cellular response to nicotine / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription coactivator binding / histone deacetylase binding / cellular response to hydrogen peroxide / cellular response to tumor necrosis factor / chromatin organization / cellular response to lipopolysaccharide / regulation of inflammatory response / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of canonical NF-kappaB signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / inflammatory response / DNA-binding transcription factor activity
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsBiswas, T. / Shahabi, S. / 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: Nucleic Acids Res. / Year: 2025
Title: Teamwork of clustered low-affinity kappa B sites and accessory factors regulates transcriptional strength of NF-kappa B RelA dimers.
Authors: Shahabi, S. / Biswas, T. / Shen, Y. / Sanahmadi, R. / Zou, Y. / Ghosh, G.
History
DepositionOct 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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


Theoretical massNumber of molelcules
Total (without water)76,7714
Polymers76,7714
Non-polymers00
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-45 kcal/mol
Surface area32090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.789, 133.081, 45.356
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: 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
#2: DNA chain DNA (5'-D(P*AP*CP*TP*GP*GP*GP*CP*TP*TP*TP*TP*CP*CP*AP*GP*TP*GP*A)-3')


Mass: 5522.577 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: DNA chain DNA (5'-D(P*TP*CP*AP*CP*TP*GP*GP*AP*AP*AP*AP*GP*CP*CP*CP*AP*GP*T)-3')


Mass: 5509.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.33 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Tris HCl 25mM pH 7.5, NaCl 50 mM, DTT 1 mM, MES 50 mM pH 5.5, CaCl2 2 mM, Spermidine 1 mM, b-D-octylglucopyranoside 0.05%, Ammonium chloride 50 mM, PEG3350 14%

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 46623 / % possible obs: 99.4 % / Redundancy: 13 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.022 / Rrim(I) all: 0.082 / Χ2: 0.858 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.03-2.0710.61.71823260.6810.90.5471.8061.19899.5
2.07-2.111.42.0422490.7920.940.6242.1360.69299.1
2.1-2.1411.31.54722690.8450.9570.4731.6210.62696.9
2.14-2.1913.31.18122680.9090.9760.3311.2280.63399.5
2.19-2.2313.21.36823070.9040.9750.3851.4220.77299.6
2.23-2.2912.90.94423140.9120.9770.2730.9831.29699.7
2.29-2.3414.10.822890.9490.9870.2170.8290.63599.8
2.34-2.4113.90.62923300.9680.9920.1720.6530.65199.9
2.41-2.4813.90.4923000.9750.9940.1340.5080.64599.7
2.48-2.5613.70.38923150.9820.9950.1070.4040.64499.8
2.56-2.6513.30.29223470.9910.9980.0820.3030.71199.8
2.65-2.76130.23623140.9930.9980.0670.2460.97399.9
2.76-2.8812.80.15123280.9960.9990.0440.1580.707100
2.88-3.0311.90.11223030.9970.9990.0330.1170.75998.1
3.03-3.2213.10.08123290.9980.9990.0230.0840.81698.4
3.22-3.4714.10.07323510.99910.020.0761.193100
3.47-3.8213.90.06223650.99910.0170.0641.188100
3.82-4.3713.50.05123870.99910.0140.0531.244100
4.37-5.5112.60.04424250.99810.0130.0460.989100
5.51-5012.50.03825070.9970.9990.0110.040.76397.7

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Processing

Software
NameVersionClassification
PHENIXdev_4788refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→37.48 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2829 1752 4.9 %
Rwork0.2438 --
obs0.2457 35763 76.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→37.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 738 0 264 5386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045315
X-RAY DIFFRACTIONf_angle_d0.7187359
X-RAY DIFFRACTIONf_dihedral_angle_d21.925969
X-RAY DIFFRACTIONf_chiral_restr0.046793
X-RAY DIFFRACTIONf_plane_restr0.007862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.10.3504390.3021595X-RAY DIFFRACTION18
2.1-2.160.3007520.2824886X-RAY DIFFRACTION26
2.16-2.230.3715570.2961423X-RAY DIFFRACTION42
2.23-2.310.3474940.33851772X-RAY DIFFRACTION53
2.31-2.40.35021270.30082365X-RAY DIFFRACTION70
2.4-2.510.34051440.29912927X-RAY DIFFRACTION86
2.51-2.640.36841750.29533343X-RAY DIFFRACTION99
2.64-2.810.38691890.29943374X-RAY DIFFRACTION100
2.81-3.020.31591660.28343436X-RAY DIFFRACTION100
3.02-3.330.26241640.24473337X-RAY DIFFRACTION98
3.33-3.810.2651970.23433455X-RAY DIFFRACTION100
3.81-4.790.22561720.1943468X-RAY DIFFRACTION100
4.8-37.480.23111760.19743630X-RAY DIFFRACTION99

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