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- PDB-2v2t: X-ray structure of a NF-kB p50-RelB-DNA complex -

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Basic information

Entry
Database: PDB / ID: 2v2t
TitleX-ray structure of a NF-kB p50-RelB-DNA complex
Components
  • 5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*CP*CP*CP)-3'
  • NUCLEAR FACTOR NF-KAPPA-B P105 SUBUNIT
  • TRANSCRIPTION FACTOR RELB
KeywordsTRANSCRIPTION / 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL / AQUIFEX AEOLICUS / NUCLEOTIDE-BINDING / ISOPRENE BIOSYNTHESIS / KINASE / TRANSFERASE / ATP-BINDING / NON-MEVALONATE
Function / homology
Function and homology information


cellular response to diterpene / cellular response to glucoside / 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 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / T-helper 1 cell differentiation / TRAF6 mediated NF-kB activation / Dectin-1 mediated noncanonical NF-kB signaling ...cellular response to diterpene / cellular response to glucoside / 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 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / T-helper 1 cell differentiation / TRAF6 mediated NF-kB activation / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / positive regulation of hyaluronan biosynthetic process / 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 / cellular response to carbohydrate stimulus / mammary gland involution / antibacterial innate immune response / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / Downstream TCR signaling / cellular response to interleukin-17 / NF-kappaB p50/p65 complex / cellular response to peptide / CD209 (DC-SIGN) signaling / myeloid dendritic cell differentiation / negative regulation of interleukin-12 production / negative regulation of interferon-beta production / cellular response to interleukin-6 / cellular response to osmotic stress / actinin binding / cellular response to dsRNA / cellular response to angiotensin / positive regulation of miRNA metabolic process / non-canonical NF-kappaB signal transduction / negative regulation of cytokine production / T-helper 1 type immune response / cellular response to cytokine stimulus / antigen processing and presentation / cellular response to organic cyclic compound / cellular response to interleukin-1 / positive regulation of transcription initiation by RNA polymerase II / lymph node development / canonical NF-kappaB signal transduction / JNK cascade / heat shock protein binding / cellular response to brain-derived neurotrophic factor stimulus / response to muscle stretch / transcription repressor complex / Neutrophil degranulation / response to cytokine / RNA polymerase II transcription regulatory region sequence-specific DNA binding / B cell receptor signaling pathway / transcription coregulator activity / circadian regulation of gene expression / cellular response to virus / response to organic cyclic compound / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / cellular response to nicotine / cellular response to mechanical stimulus / sequence-specific double-stranded DNA binding / MAPK cascade / positive regulation of canonical Wnt signaling pathway / cellular response to tumor necrosis factor / gene expression / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / sequence-specific DNA binding / transcription regulator complex / response to oxidative stress / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / innate immune response / negative regulation of DNA-templated transcription / centrosome / chromatin binding / synapse / positive regulation of gene expression / protein-containing complex binding / chromatin / negative regulation of apoptotic process / protein kinase binding / apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Transcription factor RelB / RelB leucine zipper / RelB transactivation domain / RelB leucine zipper / RelB transactivation domain / Rel homology domain (RHD), DNA-binding domain / Nuclear factor NF-kappa-B, p105 subunit / : / NF-kappa-B/Dorsal / Rel homology domain, conserved site ...Transcription factor RelB / RelB leucine zipper / RelB transactivation domain / RelB leucine zipper / RelB transactivation domain / Rel homology domain (RHD), DNA-binding domain / Nuclear factor NF-kappa-B, p105 subunit / : / 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 repeat / 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 p105 subunit / Transcription factor RelB
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsMoorthy, A.K. / Huang, D.B. / Wang, V.Y. / Vu, D. / Ghosh, G.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: X-Ray Structure of a NF-kappaB p50/Relb/DNA Complex Reveals Assembly of Multiple Dimers on Tandem kappaB Sites.
Authors: Moorthy, A.K. / Huang, D.B. / Wang, V.Y. / Vu, D. / Ghosh, G.
History
DepositionJun 7, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSCRIPTION FACTOR RELB
B: NUCLEAR FACTOR NF-KAPPA-B P105 SUBUNIT
C: 5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*CP*CP*CP)-3'
D: 5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*CP*CP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)75,9854
Polymers75,9854
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-2.9 kcal/mol
Surface area39620 Å2
MethodPQS
Unit cell
Length a, b, c (Å)91.440, 91.440, 419.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein TRANSCRIPTION FACTOR RELB / RELB


Mass: 32604.146 Da / Num. of mol.: 1 / Fragment: RESIDUES 91-378
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line: NF-KB1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q04863
#2: Protein NUCLEAR FACTOR NF-KAPPA-B P105 SUBUNIT / DNA-BINDING FACTOR KBF1 / EBP-1 / NF-KAPPA-B1 P84/NF-KAPPA-B1 P98 / P50


Mass: 36712.926 Da / Num. of mol.: 1
Fragment: NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT, RESIDUES 38-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line: NF-KB1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P25799
#3: DNA chain 5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*CP*CP*CP)-3'


Mass: 3334.186 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.34 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 7
Details: 5% PEG3350 100 MM NACITRATE 1MM SPERMINE 5MM DTT, pH 7

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.05
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 3.04→30 Å / Num. obs: 19931 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Biso Wilson estimate: 86 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12
Reflection shellResolution: 3.04→3.15 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.5 / % possible all: 91

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VKX

1vkx


Resolution: 3.05→19.9 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 89352.41 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.276 916 4.8 %RANDOM
Rwork0.238 ---
obs0.238 19087 91.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.5829 Å2 / ksol: 0.212846 e/Å3
Displacement parametersBiso mean: 74 Å2
Baniso -1Baniso -2Baniso -3
1-10.87 Å220.2 Å20 Å2
2--10.87 Å20 Å2
3----21.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3.05→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4658 442 0 34 5134
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
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: 3.05→3.24 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.382 117 4.5 %
Rwork0.329 2502 -
obs--78.6 %
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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