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- PDB-9bdv: NF-kappaB RelA homo-dimer bound to TA-centric kappaB DNA -

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Basic information

Entry
Database: PDB / ID: 9bdv
TitleNF-kappaB RelA homo-dimer bound to TA-centric kappaB DNA
Components
  • DNA (5'-D(*AP*TP*CP*AP*CP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*AP*GP*T)-3')
  • DNA (5'-D(P*AP*CP*TP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*AP*GP*TP*GP*AP*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 / prolactin signaling pathway / Downstream TCR signaling / 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 / cellular response to nicotine / positive regulation of interleukin-6 production / 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 / cellular response to lipopolysaccharide / chromatin organization / 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)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBiswas, T. / Shahabi, S. / Tsodikov, O.V.
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*TP*TP*TP*CP*CP*AP*GP*TP*GP*AP*T)-3')
D: DNA (5'-D(*AP*TP*CP*AP*CP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*AP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7718
Polymers77,3874
Non-polymers3844
Water10,863603
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint-119 kcal/mol
Surface area31880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.654, 132.682, 45.663
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*AP*AP*TP*TP*TP*CP*CP*AP*GP*TP*GP*AP*T)-3')


Mass: 5859.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*AP*TP*CP*AP*CP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*AP*GP*T)-3')


Mass: 5788.773 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / Source method: isolated from a natural source / Formula: H2O
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: 2.32 Å3/Da / Density % sol: 47.04 %
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 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 57610 / % possible obs: 99.6 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.994 / Χ2: 0.047 / Net I/σ(I): 8.5 / Num. measured all: 448525
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.9-1.937.72.55829610.991199.9
1.93-1.977.81.88630010.871199.8
1.97-2.017.71.38229800.879199.8
2.01-2.067.81.18529940.91199.8
2.06-2.17.70.88329941.0581100
2.1-2.167.90.69330230.928199.9
2.16-2.217.80.60629830.903199.9
2.21-2.287.80.56630371.0871100
2.28-2.357.90.41229980.8941100
2.35-2.447.90.32130180.8961100
2.44-2.537.90.23330530.8631100
2.53-2.6580.17730180.8611100
2.65-2.7980.13730130.9361100
2.79-2.9680.130620.8961100
2.96-3.1980.07830511.0171100
3.19-3.517.90.06730981.2771100
3.51-4.027.70.05430781.1091100
4.02-5.067.50.0431270.778199.8
5.06-306.90.04431210.836194.4

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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: 1.9→29.66 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.212 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23048 2577 4.9 %RANDOM
Rwork0.19109 ---
obs0.19302 49976 90.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.612 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0 Å2
2---0.04 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.9→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 740 20 603 5747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0125334
X-RAY DIFFRACTIONr_bond_other_d0.0090.0164403
X-RAY DIFFRACTIONr_angle_refined_deg0.9611.6937393
X-RAY DIFFRACTIONr_angle_other_deg0.3621.56210356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3425548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.946550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47410753
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.2797
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025657
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02989
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_it0.9352.5432198
X-RAY DIFFRACTIONr_mcbond_other0.9342.5432198
X-RAY DIFFRACTIONr_mcangle_it1.2233.8032744
X-RAY DIFFRACTIONr_mcangle_other1.2233.8062745
X-RAY DIFFRACTIONr_scbond_it1.2613.5133136
X-RAY DIFFRACTIONr_scbond_other1.2563.5073121
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6855.2234626
X-RAY DIFFRACTIONr_long_range_B_refined2.91644.3366159
X-RAY DIFFRACTIONr_long_range_B_other2.69842.6075985
X-RAY DIFFRACTIONr_rigid_bond_restr1.14639703
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 99 -
Rwork0.261 1724 -
obs--43.71 %

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