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- PDB-9bdu: NF-kappaB RelA homo-dimer bound to AT-centric kappaB DNA -

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Basic information

Entry
Database: PDB / ID: 9bdu
TitleNF-kappaB RelA homo-dimer bound to AT-centric kappaB DNA
Components
  • DNA (5'-D(P*AP*CP*TP*GP*GP*GP*AP*AP*AP*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*TP*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 / positive regulation of chondrocyte differentiation / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / acetaldehyde metabolic process / prolactin signaling pathway / Downstream TCR signaling / 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 / cellular response to interleukin-6 / nucleotide-binding oligomerization domain containing 2 signaling pathway / actinin binding / cellular response to angiotensin / negative regulation of non-canonical NF-kappaB signal transduction / response to UV-B / NF-kappaB complex / positive regulation of leukocyte adhesion to vascular endothelial cell / interleukin-1-mediated signaling pathway / non-canonical NF-kappaB signal transduction / 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 / positive regulation of T cell receptor signaling pathway / response to cobalamin / phosphate ion binding / cellular response to lipoteichoic acid / response to muramyl dipeptide / general transcription initiation factor binding / NF-kappaB binding / positive regulation of vascular endothelial growth factor production / hair follicle development / neuropeptide signaling pathway / response to amino acid / RNA polymerase II core promoter sequence-specific DNA binding / canonical NF-kappaB signal transduction / negative regulation of insulin receptor signaling pathway / tumor necrosis factor-mediated signaling pathway / response to cAMP / response to muscle stretch / positive regulation of interleukin-12 production / negative regulation of angiogenesis / liver development / negative regulation of miRNA transcription / response to cytokine / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / response to ischemia / response to progesterone / negative regulation of extrinsic apoptotic signaling pathway / animal organ morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / response to bacterium / peptide binding / response to insulin / protein catabolic process / negative regulation of protein catabolic process / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription coactivator binding / defense response / positive regulation of miRNA transcription / histone deacetylase binding / cellular response to hydrogen peroxide / cellular response to nicotine / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to tumor necrosis factor / chromatin organization / positive regulation of NF-kappaB transcription factor activity / regulation of inflammatory response / double-stranded DNA binding / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / positive regulation of canonical NF-kappaB signal transduction / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / response to xenobiotic stimulus / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / innate immune response / DNA-templated transcription
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsBiswas, T. / 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*AP*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*TP*TP*TP*CP*CP*CP*AP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6757
Polymers77,3874
Non-polymers2883
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-97 kcal/mol
Surface area32310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.516, 133.568, 45.443
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*AP*TP*TP*CP*CP*AP*GP*TP*GP*AP*T)-3')


Mass: 5868.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*TP*CP*AP*CP*TP*GP*GP*AP*AP*TP*TP*TP*CP*CP*CP*AP*GP*T)-3')


Mass: 5779.759 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, MES, beta-octylglucoside, spermine / PH range: 5-6.5

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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: 2.03→30 Å / Num. obs: 46270 / % possible obs: 99.7 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.994 / Χ2: 0.03 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.03-2.0610.82.3222860.797199.1
2.06-2.111.31.70722600.897199.8
2.1-2.1411.71.66322680.792199.9
2.14-2.1911.91.64222900.8271100
2.19-2.2311.91.62822710.8481100
2.23-2.2911.91.30522870.9771100
2.29-2.34121.19622790.8611100
2.34-2.4112.20.89523030.868199.9
2.41-2.4812.20.77523020.8751100
2.48-2.5612.20.56622930.91100
2.56-2.6512.20.40523080.9041100
2.65-2.7512.30.29423030.9871100
2.75-2.8812.30.20823200.9861100
2.88-3.0312.50.16123381.0721100
3.03-3.2212.70.11722931.2951100
3.22-3.4712.70.09623461.6891100
3.47-3.8212.60.08123511.7431100
3.82-4.3712.30.06323411.5721100
4.37-5.512.30.05224031.2931100
5.5-3011.50.05124281.035195.4

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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: 2.03→28.91 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.906 / SU B: 14.363 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2733 1739 5 %RANDOM
Rwork0.22322 ---
obs0.22573 33225 75.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.057 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.03→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 781 15 397 5577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125376
X-RAY DIFFRACTIONr_bond_other_d0.0260.0164427
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.6947457
X-RAY DIFFRACTIONr_angle_other_deg0.8451.56110414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3145548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.656550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02210754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2805
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025672
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02995
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_it0.413.5762198
X-RAY DIFFRACTIONr_mcbond_other0.413.5762198
X-RAY DIFFRACTIONr_mcangle_it0.4975.352744
X-RAY DIFFRACTIONr_mcangle_other0.4975.3522745
X-RAY DIFFRACTIONr_scbond_it0.4284.2343178
X-RAY DIFFRACTIONr_scbond_other0.4244.2243167
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.5126.2844696
X-RAY DIFFRACTIONr_long_range_B_refined1.16755.6066198
X-RAY DIFFRACTIONr_long_range_B_other1.12154.4586124
X-RAY DIFFRACTIONr_rigid_bond_restr2.62739767
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 23 -
Rwork0.268 489 -
obs--15.25 %

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