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- PDB-3do7: X-ray structure of a NF-kB p52/RelB/DNA complex -

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Basic information

Entry
Database: PDB / ID: 3do7
TitleX-ray structure of a NF-kB p52/RelB/DNA complex
Components
  • 5'-D(*DCP*DGP*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DC)-3'
  • Avian reticuloendotheliosis viral (V-rel) oncogene related B
  • Nuclear factor NF-kappa-B p100 subunit
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / Nucleus / Activator / Alternative splicing / ANK repeat / Chromosomal rearrangement / Cytoplasm / Disease mutation / DNA-binding / Phosphoprotein / Polymorphism / Proto-oncogene / Transcription / Transcription regulation / Ubl conjugation / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / T-helper 1 cell differentiation / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / lymphocyte differentiation / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / chromatin => GO:0000785 / IkBA variant leads to EDA-ID / CD209 (DC-SIGN) signaling ...follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / T-helper 1 cell differentiation / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / lymphocyte differentiation / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / chromatin => GO:0000785 / IkBA variant leads to EDA-ID / CD209 (DC-SIGN) signaling / myeloid dendritic cell differentiation / germinal center formation / negative regulation of interferon-beta production / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / cellular response to osmotic stress / Interleukin-1 processing / T-helper 1 type immune response / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation / The NLRP3 inflammasome / antigen processing and presentation / canonical NF-kappaB signal transduction / Purinergic signaling in leishmaniasis infection / spleen development / transcription repressor complex / extracellular matrix organization / NIK-->noncanonical NF-kB signaling / response to cytokine / Dectin-1 mediated noncanonical NF-kB signaling / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / TAK1-dependent IKK and NF-kappa-B activation / PKMTs methylate histone lysines / rhythmic process / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / response to lipopolysaccharide / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / centrosome / negative regulation of DNA-templated transcription / synapse / host cell nucleus / chromatin binding / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / protein kinase binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Transcription factor RelB / Nuclear factor NF-kappa-B, p100 subunit / RelB leucine zipper / RelB transactivation domain / RelB leucine zipper / RelB transactivation domain / Rel homology domain (RHD), DNA-binding domain / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain ...Transcription factor RelB / Nuclear factor NF-kappa-B, p100 subunit / RelB leucine zipper / RelB transactivation domain / RelB leucine zipper / RelB transactivation domain / Rel homology domain (RHD), DNA-binding domain / 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 / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Death-like domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear factor NF-kappa-B p100 subunit / Transcription factor RelB / Transcription factor RelB
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsFusco, A. / Huang, D.B. / Miller, D. / Vu, D. / Ghosh, G.
CitationJournal: TO BE PUBLISHED
Title: NF-kapppaB p52:RelB heterodimer uses different binding modes to recognize different kappaB DNA
Authors: Fusco, A. / Huang, D.B. / Miller, D. / Vu, D. / Ghosh, G.
History
DepositionJul 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*DCP*DGP*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DC)-3'
D: 5'-D(*DCP*DGP*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DC)-3'
E: 5'-D(*DCP*DGP*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DC)-3'
A: Avian reticuloendotheliosis viral (V-rel) oncogene related B
B: Nuclear factor NF-kappa-B p100 subunit


Theoretical massNumber of molelcules
Total (without water)76,5405
Polymers76,5405
Non-polymers00
Water88349
1
C: 5'-D(*DCP*DGP*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DC)-3'
D: 5'-D(*DCP*DGP*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DC)-3'
A: Avian reticuloendotheliosis viral (V-rel) oncogene related B
B: Nuclear factor NF-kappa-B p100 subunit


Theoretical massNumber of molelcules
Total (without water)73,2064
Polymers73,2064
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-34.9 kcal/mol
Surface area34880 Å2
MethodPISA
2
E: 5'-D(*DCP*DGP*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DC)-3'

E: 5'-D(*DCP*DGP*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DC)-3'


Theoretical massNumber of molelcules
Total (without water)6,6682
Polymers6,6682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area840 Å2
ΔGint-10.7 kcal/mol
Surface area4520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.640, 124.130, 189.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: DNA chain 5'-D(*DCP*DGP*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DCP*DC)-3'


Mass: 3334.186 Da / Num. of mol.: 3 / Fragment: kappa B site / Source method: obtained synthetically / Details: kappaB DNA
#2: Protein Avian reticuloendotheliosis viral (V-rel) oncogene related B


Mass: 33514.039 Da / Num. of mol.: 1 / Fragment: RHR (UNP residues 88-383)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Relb / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8VE46, UniProt: Q04863*PLUS
#3: Protein Nuclear factor NF-kappa-B p100 subunit / DNA-binding factor KBF2 / H2TF1 / Lymphocyte translocation chromosome 10 / Oncogene Lyt-10 / Lyt10 ...DNA-binding factor KBF2 / H2TF1 / Lymphocyte translocation chromosome 10 / Oncogene Lyt-10 / Lyt10 / Nuclear factor NF-kappa-B p52 subunit


Mass: 33023.820 Da / Num. of mol.: 1 / Fragment: RHR (UNP residues 37-329)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFKB2, LYT10 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q00653
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 6% PEG 4000, 50 mM NaCl, 0.1% BOG, 10 mM DTT, 10 mM NaCitrate and 2 mM Spermidine, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2NaClSodium chloride11
3BOG11
4DTT11
5NaCitrate11
6Spermidine11
7PEG 400012
8NaClSodium chloride12
9BOG12
10DTT12
11NaCitrate12
12Spermidine12

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Data collection

DiffractionMean temperature: 106 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorDetector: CCD / Date: Jan 1, 2005 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.05→30 Å / Num. obs: 16342 / % possible obs: 91.7 % / Observed criterion σ(I): 1 / Redundancy: 14 % / Biso Wilson estimate: 85.7 Å2 / Rsym value: 0.064 / Net I/σ(I): 14.4
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 12 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 1045 / Rsym value: 0.47 / % possible all: 60

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→29.19 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 53121.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.273 851 5.9 %RANDOM
Rwork0.23 ---
obs0.23 14478 81.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10.1666 Å2 / ksol: 0.196009 e/Å3
Displacement parametersBiso mean: 97.9 Å2
Baniso -1Baniso -2Baniso -3
1-30.17 Å20 Å20 Å2
2---21.71 Å20 Å2
3----8.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 3.05→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4595 644 0 49 5288
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d1.07
LS refinement shellResolution: 3.05→3.24 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 62 5.3 %
Rwork0.267 1114 -
obs--40.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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