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- PDB-2ram: A NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER -

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Basic information

Entry
Database: PDB / ID: 2ram
TitleA NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER
Components
  • DNA (5'-D(*CP*GP*GP*CP*TP*GP*GP*AP*AP*AP*TP*(5IU)P*(5IU)P*CP*CP*AP*GP*CP*CP*G)-3')
  • PROTEIN (TRANSCRIPTION FACTOR NF-KB P65)
KeywordsTRANSCRIPTION/DNA / COMPLEX (TRANSCRIPTION FACTOR-DNA) / DNA-BINDING / TRANSCRIPTION REGULATION / ACTIVATOR NUCLEAR PROTEIN / PHOSPHORYLATION / CONFORMATION / 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 / positive regulation of Schwann cell differentiation / PKMTs methylate histone lysines / NF-kB is activated and signals survival / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells ...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 / positive regulation of Schwann cell differentiation / PKMTs methylate histone lysines / NF-kB is activated and signals survival / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / TAK1-dependent IKK and NF-kappa-B activation / Activation of NF-kappaB in B cells / positive regulation of chondrocyte differentiation / prolactin signaling pathway / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / NF-kappaB p50/p65 complex / Interleukin-1 signaling / toll-like receptor TLR6:TLR2 signaling pathway / Downstream TCR signaling / CD209 (DC-SIGN) signaling / cellular response to peptidoglycan / ankyrin repeat binding / nucleotide-binding oligomerization domain containing 2 signaling pathway / negative regulation of protein sumoylation / postsynapse to nucleus signaling pathway / defense response to tumor cell / positive regulation of T cell receptor signaling pathway / signal transduction involved in regulation of gene expression / cellular response to interleukin-6 / actinin binding / negative regulation of non-canonical NF-kappaB signal transduction / response to UV-B / positive regulation of miRNA metabolic process / interleukin-1-mediated signaling pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / toll-like receptor 4 signaling pathway / cellular response to hepatocyte growth factor stimulus / vascular endothelial growth factor signaling pathway / NF-kappaB complex / positive regulation of amyloid-beta formation / non-canonical NF-kappaB signal transduction / phosphate ion binding / cellular response to lipoteichoic acid / response to muramyl dipeptide / cellular response to angiotensin / hair follicle development / positive regulation of vascular endothelial growth factor production / cellular response to interleukin-1 / general transcription initiation factor binding / NF-kappaB binding / RNA polymerase II core promoter sequence-specific DNA binding / response to muscle stretch / peptide binding / positive regulation of interleukin-12 production / canonical NF-kappaB signal transduction / negative regulation of insulin receptor signaling pathway / negative regulation of cytokine production involved in inflammatory response / response to cytokine / negative regulation of miRNA transcription / response to interleukin-1 / antiviral innate immune response / negative regulation of angiogenesis / animal organ morphogenesis / tumor necrosis factor-mediated signaling pathway / : / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / RNA polymerase II transcription regulatory region sequence-specific DNA binding / response to bacterium / neuropeptide signaling pathway / liver development / defense response / negative regulation of protein catabolic process / chromatin DNA binding / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to nicotine / positive regulation of interleukin-6 production / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to tumor necrosis factor / transcription coactivator binding / histone deacetylase binding / cellular response to hydrogen peroxide / cytokine-mediated signaling pathway / chromatin organization / cellular response to lipopolysaccharide / regulation of inflammatory response / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / DNA-binding transcription factor binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / transcription cis-regulatory region binding / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / DNA / DNA (> 10) / Transcription factor p65
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsChen, Y.Q. / Ghosh, S. / Ghosh, G.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: A novel DNA recognition mode by the NF-kappa B p65 homodimer.
Authors: Chen, Y.Q. / Ghosh, S. / Ghosh, G.
History
DepositionNov 23, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*CP*GP*GP*CP*TP*GP*GP*AP*AP*AP*TP*(5IU)P*(5IU)P*CP*CP*AP*GP*CP*CP*G)-3')
D: DNA (5'-D(*CP*GP*GP*CP*TP*GP*GP*AP*AP*AP*TP*(5IU)P*(5IU)P*CP*CP*AP*GP*CP*CP*G)-3')
A: PROTEIN (TRANSCRIPTION FACTOR NF-KB P65)
B: PROTEIN (TRANSCRIPTION FACTOR NF-KB P65)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0466
Polymers74,7384
Non-polymers3092
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.810, 80.620, 167.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*CP*GP*GP*CP*TP*GP*GP*AP*AP*AP*TP*(5IU)P*(5IU)P*CP*CP*AP*GP*CP*CP*G)-3')


Mass: 6358.706 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein PROTEIN (TRANSCRIPTION FACTOR NF-KB P65) / RELA


Mass: 31010.080 Da / Num. of mol.: 2 / Fragment: P65 RESIDUES 19 - 291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q04207
#3: Chemical ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mM1dropCaCl2
27.5 mg/mlDNA complex1drop
34 %PEG33501drop
45 mMdithiothreitol1drop
50.05 %beta-octyl glucopyranoside1drop
625 mMHEPES1drop
78 %PEG33501reservoir
8100 mM1reservoirCaCl2
910 mMdithiothreitol1reservoir
100.1 %beta-octyl glucopyranoside1reservoir
1150 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 31656 / % possible obs: 90 % / Redundancy: 3.3 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.053
Reflection
*PLUS
Num. measured all: 103396

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Processing

Software
NameVersionClassification
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.4→6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.308 2752 10.2 %RANDOM
Rwork0.213 ---
obs0.213 27086 81.4 %-
Displacement parametersBiso mean: 45.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.32 Å
Luzzati d res low-6 Å
Luzzati sigma a0.49 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4356 810 20 128 5314
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.62
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.561.5
X-RAY DIFFRACTIONx_mcangle_it4.082
X-RAY DIFFRACTIONx_scbond_it3.812
X-RAY DIFFRACTIONx_scangle_it5.592.5
LS refinement shellResolution: 2.4→2.54 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.385 297 10.2 %
Rwork0.346 2621 -
obs--53 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.62

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