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- PDB-1svc: NFKB P50 HOMODIMER BOUND TO DNA -

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Basic information

Entry
Database: PDB / ID: 1svc
TitleNFKB P50 HOMODIMER BOUND TO DNA
Components
  • DNA (5'-D(*AP*GP*AP*TP*GP*GP*GP*GP*AP*AP*TP*CP*CP*CP*CP*TP*A P*GP*A)-3')
  • PROTEIN (NUCLEAR FACTOR KAPPA-B (NF-KB))
KeywordsTRANSCRIPTION/DNA / DNA-BINDING / TRANSCRIPTION REGULATION / ACTIVATOR / NUCLEAR PROTEIN / PHOSPHORYLATION / DNA / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


negative regulation of calcidiol 1-monooxygenase activity / negative regulation of vitamin D biosynthetic process / I-kappaB/NF-kappaB complex / negative regulation of cholesterol transport / positive regulation of hyaluronan biosynthetic process / antibacterial innate immune response / mammary gland involution / cellular response to interleukin-17 / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex ...negative regulation of calcidiol 1-monooxygenase activity / negative regulation of vitamin D biosynthetic process / I-kappaB/NF-kappaB complex / negative regulation of cholesterol transport / positive regulation of hyaluronan biosynthetic process / antibacterial innate immune response / mammary gland involution / cellular response to interleukin-17 / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / positive regulation of macrophage derived foam cell differentiation / positive regulation of lipid storage / negative regulation of interleukin-12 production / Regulated proteolysis of p75NTR / RIP-mediated NFkB activation via ZBP1 / CLEC7A/inflammasome pathway / cellular response to dsRNA / Interleukin-1 processing / cellular response to interleukin-6 / actinin binding / cellular response to angiotensin / Regulation of NFE2L2 gene expression / negative regulation of protein metabolic process / positive regulation of miRNA metabolic process / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation / The NLRP3 inflammasome / Transcriptional Regulation by VENTX / positive regulation of transcription initiation by RNA polymerase II / canonical NF-kappaB signal transduction / cellular response to interleukin-1 / Purinergic signaling in leishmaniasis infection / JNK cascade / response to muscle stretch / NF-kB is activated and signals survival / CD209 (DC-SIGN) signaling / MAP3K8 (TPL2)-dependent MAPK1/3 activation / response to cytokine / Activation of NF-kappaB in B cells / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / B cell receptor signaling pathway / TAK1-dependent IKK and NF-kappa-B activation / CLEC7A (Dectin-1) signaling / PKMTs methylate histone lysines / cellular response to virus / DNA-binding transcription repressor activity, RNA polymerase II-specific / FCERI mediated NF-kB activation / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Interleukin-1 signaling / HCMV Early Events / cellular response to mechanical stimulus / cellular response to nicotine / specific granule lumen / positive regulation of canonical Wnt signaling pathway / SARS-CoV-1 activates/modulates innate immune responses / Downstream TCR signaling / cellular response to tumor necrosis factor / Senescence-Associated Secretory Phenotype (SASP) / DNA-binding transcription activator activity, RNA polymerase II-specific / secretory granule lumen / cellular response to lipopolysaccharide / transcription regulator complex / transcription by RNA polymerase II / transcription cis-regulatory region binding / 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 / negative regulation of gene expression / innate immune response / apoptotic process / chromatin binding / chromatin / Neutrophil degranulation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsMueller, C.W. / Harrison, S.C.
CitationJournal: Nature / Year: 1995
Title: Structure of the NF-kappa B p50 homodimer bound to DNA.
Authors: Muller, C.W. / Rey, F.A. / Sodeoka, M. / Verdine, G.L. / Harrison, S.C.
History
DepositionNov 27, 1995Processing site: NDB
Revision 1.0Jun 10, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: DNA (5'-D(*AP*GP*AP*TP*GP*GP*GP*GP*AP*AP*TP*CP*CP*CP*CP*TP*A P*GP*A)-3')
P: PROTEIN (NUCLEAR FACTOR KAPPA-B (NF-KB))


Theoretical massNumber of molelcules
Total (without water)47,0082
Polymers47,0082
Non-polymers00
Water1,13563
1
D: DNA (5'-D(*AP*GP*AP*TP*GP*GP*GP*GP*AP*AP*TP*CP*CP*CP*CP*TP*A P*GP*A)-3')
P: PROTEIN (NUCLEAR FACTOR KAPPA-B (NF-KB))

D: DNA (5'-D(*AP*GP*AP*TP*GP*GP*GP*GP*AP*AP*TP*CP*CP*CP*CP*TP*A P*GP*A)-3')
P: PROTEIN (NUCLEAR FACTOR KAPPA-B (NF-KB))


Theoretical massNumber of molelcules
Total (without water)94,0154
Polymers94,0154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)137.000, 137.000, 57.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 5878.824 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein PROTEIN (NUCLEAR FACTOR KAPPA-B (NF-KB))


Mass: 41128.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Keywords: MUTANT C62A / References: UniProt: P19838
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 600011
3NACLSodium chloride11
4HEPES11
5DTT11
Crystal grow
*PLUS
pH: 4.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.18 mMprotein dimer1drop
20.22 mMDNA duplex1drop
30.1 M1dropNaCl
410 mM1drop
550 mMsodium acetate1reservoir
650 mM1reservoirMgCl2
71 mMdithiothreitol1reservoir
82 mMspermine1reservoir
91-4 %PEG30001reservoir

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Data collection

DiffractionMean temperature: 113 K
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→12 Å / Num. obs: 15658
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 12 Å / Rmerge(I) obs: 0.045

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.6→12 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.286 --
Rwork0.225 --
obs0.225 15648 92 %
Refinement stepCycle: LAST / Resolution: 2.6→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2449 391 0 63 2903
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 12 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.8

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