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- PDB-1u41: Crystal structure of YLGV mutant of dimerisation domain of NF-kB ... -

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Basic information

Entry
Database: PDB / ID: 1u41
TitleCrystal structure of YLGV mutant of dimerisation domain of NF-kB p50 transcription factor
ComponentsNuclear factor NF-kappa-B p105 subunit
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR / NF-KB / DIMERIZATION DOMAIN / INTERTWINED FOLDING
Function / homology
Function and homology information


Regulated proteolysis of p75NTR / I-kappaB/NF-kappaB complex / negative regulation of vitamin D biosynthetic process / 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 / TRAF6 mediated NF-kB activation / positive regulation of hyaluronan biosynthetic process / NF-kB is activated and signals survival ...Regulated proteolysis of p75NTR / I-kappaB/NF-kappaB complex / negative regulation of vitamin D biosynthetic process / 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 / TRAF6 mediated NF-kB activation / 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 / mammary gland involution / 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 / antibacterial innate immune response / Downstream TCR signaling / cellular response to interleukin-17 / NF-kappaB p50/p65 complex / CD209 (DC-SIGN) signaling / positive regulation of lipid storage / negative regulation of interleukin-12 production / cellular response to interleukin-6 / positive regulation of macrophage derived foam cell differentiation / cellular response to dsRNA / actinin binding / non-canonical NF-kappaB signal transduction / positive regulation of miRNA metabolic process / signal transduction involved in regulation of gene expression / negative regulation of cytokine production / cellular response to cytokine stimulus / cellular response to angiotensin / canonical NF-kappaB signal transduction / positive regulation of cholesterol efflux / positive regulation of transcription initiation by RNA polymerase II / lymph node development / JNK cascade / response to muscle stretch / Neutrophil degranulation / negative regulation of cytokine production involved in inflammatory response / B cell receptor signaling pathway / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cellular response to mechanical stimulus / cellular response to virus / cellular response to nicotine / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to tumor necrosis factor / positive regulation of canonical Wnt signaling pathway / MAPK cascade / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / gene expression / sequence-specific DNA binding / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / apoptotic process / chromatin binding / chromatin / 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 / cytoplasm / cytosol
Similarity search - Function
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 ...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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Nuclear factor NF-kappa-B p105 subunit
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.202 Å
AuthorsChirgadze, D.Y. / Demydchuk, M. / Becker, M. / Moran, S. / Paoli, M.
CitationJournal: Structure / Year: 2004
Title: Snapshot of Protein Structure Evolution Reveals Conservation of Functional Dimerization through Intertwined Folding
Authors: Chirgadze, D.Y. / Demydchuk, M. / Becker, M. / Moran, S. / Paoli, M.
History
DepositionJul 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Oct 20, 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 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear factor NF-kappa-B p105 subunit
B: Nuclear factor NF-kappa-B p105 subunit
C: Nuclear factor NF-kappa-B p105 subunit
D: Nuclear factor NF-kappa-B p105 subunit


Theoretical massNumber of molelcules
Total (without water)48,9714
Polymers48,9714
Non-polymers00
Water6,936385
1
A: Nuclear factor NF-kappa-B p105 subunit
B: Nuclear factor NF-kappa-B p105 subunit


Theoretical massNumber of molelcules
Total (without water)24,4862
Polymers24,4862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Nuclear factor NF-kappa-B p105 subunit
D: Nuclear factor NF-kappa-B p105 subunit


Theoretical massNumber of molelcules
Total (without water)24,4862
Polymers24,4862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.602, 73.586, 138.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsCHAINS A AND B COMPRIZE THE BIOLOGICAL DIMER / CHAINS C AND D COMPRIZE THE BIOLOGICAL DIMER

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Components

#1: Protein
Nuclear factor NF-kappa-B p105 subunit / NF-kB p50 transcription factor / DNA-binding factor KBF1 / EBP- 1 / NF-kappa-B1 p84/NF-kappa-B1 p98 ...NF-kB p50 transcription factor / DNA-binding factor KBF1 / EBP- 1 / NF-kappa-B1 p84/NF-kappa-B1 p98 [Contains: Nuclear factor NF- kappa-B p50 subunit]


Mass: 12242.806 Da / Num. of mol.: 4 / Fragment: dimerization domain / Mutation: A308G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nfkb1, 18033 / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P25799
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 1.96 Å3/Da / Density % sol: 36.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, ammonium sulphate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2002 / Details: OSMIC MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→69.01 Å / Num. all: 20980 / Num. obs: 20980 / % possible obs: 98.3 % / Observed criterion σ(I): 2.5 / Redundancy: 5.1 % / Biso Wilson estimate: 29.295 Å2 / Rsym value: 0.065 / Net I/σ(I): 14.6
Reflection shellResolution: 2.2→2.25 Å / Rmerge(I) obs: 0.281 / % possible all: 96

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BFS

1bfs


Resolution: 2.202→69.01 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.194 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.332 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1081 5.2 %RANDOM
Rwork0.173 ---
all0.176 19850 --
obs0.176 19850 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å20 Å2
2---0.32 Å20 Å2
3---1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.202→69.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3306 0 0 385 3691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223382
X-RAY DIFFRACTIONr_bond_other_d0.0020.023028
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.9634557
X-RAY DIFFRACTIONr_angle_other_deg0.86437080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6225396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023700
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02716
X-RAY DIFFRACTIONr_nbd_refined0.1930.2630
X-RAY DIFFRACTIONr_nbd_other0.2550.23596
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.21957
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.2238
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3330.2102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it3.01552012
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.00463272
X-RAY DIFFRACTIONr_scbond_it3.68251370
X-RAY DIFFRACTIONr_scangle_it5.1727.51285
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.31 70
Rwork0.191 1373

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