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- PDB-5u01: Cooperative DNA binding by two RelA dimers -

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Basic information

Entry
Database: PDB / ID: 5u01
TitleCooperative DNA binding by two RelA dimers
Components
  • DNA (27-MER)
  • Transcription factor p65
KeywordsTRANSCRIPTION/DNA / NF-kB / DNA binding / TRANSCRIPTION-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 / FCERI mediated NF-kB activation / positive regulation of chondrocyte differentiation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / acetaldehyde metabolic process / Downstream TCR signaling / prolactin signaling pathway / NF-kappaB p50/p65 complex / positive regulation of Schwann cell differentiation / CD209 (DC-SIGN) signaling / cellular response to peptidoglycan / ankyrin repeat binding / negative regulation of protein sumoylation / postsynapse to nucleus signaling pathway / defense response to tumor cell / nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to interleukin-6 / actinin binding / negative regulation of non-canonical NF-kappaB signal transduction / NF-kappaB complex / cellular response to angiotensin / response to UV-B / vascular endothelial growth factor signaling pathway / interleukin-1-mediated signaling pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / positive regulation of miRNA metabolic process / toll-like receptor 4 signaling pathway / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / positive regulation of T cell receptor signaling pathway / response to cobalamin / phosphate ion binding / non-canonical NF-kappaB signal transduction / cellular response to lipoteichoic acid / response to muramyl dipeptide / general transcription initiation factor binding / NF-kappaB binding / hair follicle development / neuropeptide signaling pathway / positive regulation of vascular endothelial growth factor production / RNA polymerase II core promoter sequence-specific DNA binding / canonical NF-kappaB signal transduction / response to amino acid / cellular response to interleukin-1 / negative regulation of insulin receptor signaling pathway / response to cAMP / tumor necrosis factor-mediated signaling pathway / response to muscle stretch / positive regulation of interleukin-12 production / response to interleukin-1 / negative regulation of angiogenesis / negative regulation of miRNA transcription / liver development / response to progesterone / response to organic substance / positive regulation of interleukin-1 beta production / response to cytokine / response to ischemia / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / response to bacterium / peptide binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / protein catabolic process / response to insulin / defense response / transcription coactivator binding / negative regulation of protein catabolic process / chromatin DNA binding / cellular response to hydrogen peroxide / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / cytokine-mediated signaling pathway / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to nicotine / histone deacetylase binding / cellular response to tumor necrosis factor / chromatin organization / positive regulation of NF-kappaB transcription factor activity / regulation of inflammatory response / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / positive regulation of canonical NF-kappaB signal transduction / DNA-binding transcription factor binding / cellular response to lipopolysaccharide / transcription regulator complex / sequence-specific DNA binding / transcription cis-regulatory region binding
Similarity search - Function
Rel homology domain (RHD), DNA-binding domain / 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 ...Rel homology domain (RHD), DNA-binding domain / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor p65
Similarity search - Component
Biological speciesMus musculus (house mouse)
Synthesium (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGhosh, G. / Huang, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 085490 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: DNA-binding affinity and transcriptional activity of the RelA homodimer of nuclear factor kappa B are not correlated.
Authors: Mulero, M.C. / Huang, D.B. / Nguyen, H.T. / Wang, V.Y. / Li, Y. / Biswas, T. / Ghosh, G.
History
DepositionNov 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Transcription factor p65
D: Transcription factor p65
F: DNA (27-MER)
E: DNA (27-MER)


Theoretical massNumber of molelcules
Total (without water)140,6256
Polymers140,6256
Non-polymers00
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13000 Å2
ΔGint-80 kcal/mol
Surface area58180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.910, 117.800, 70.810
Angle α, β, γ (deg.)90.00, 91.20, 90.00
Int Tables number4
Space group name H-MP1211

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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: 31010.080 Da / Num. of mol.: 4 / Fragment: UNP residues 19-291 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q04207
#2: DNA chain DNA (27-MER)


Mass: 8292.346 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthesium (invertebrata)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.64 Å3/Da / Density % sol: 53.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: Nacit 5.5 100mM, CaCl2 10mM, DTT 10mM, PEG 3350 15%.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.988 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 50721 / % possible obs: 99 % / Redundancy: 3.4 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 13.1
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ram

2ram


Resolution: 2.5→29.63 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 120710.55 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 1 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.274 2157 5 %RANDOM
Rwork0.221 ---
obs0.221 43116 85.4 %-
Solvent computationBsol: 44.2308 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 81.9 Å2
Baniso -1Baniso -2Baniso -3
1-11.63 Å20 Å2-3.24 Å2
2---29.99 Å20 Å2
3---18.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.6 Å
Refinement stepCycle: 1 / Resolution: 2.5→29.63 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms0 0 0 0 0
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
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
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.422 259 5 %
Rwork0.39 4890 -
obs--61.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/protein_rep.paramCNS_TOPPAR/protein.top
X-RAY DIFFRACTION2CNS_TOPPAR/dna-rna_rep.paramCNS_TOPPAR/dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR/water_rep.paramCNS_TOPPAR/water.top
X-RAY DIFFRACTION4CNS_TOPPAR/ion.paramCNS_TOPPAR/ion.top
X-RAY DIFFRACTION8&_1_PARAMETER_INFILE_8&_1_TOPOLOGY_INFILE_8

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