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- PDB-3jv5: Crystal structure of the dimerization domains p52 homodimer -

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Basic information

Entry
Database: PDB / ID: 3jv5
TitleCrystal structure of the dimerization domains p52 homodimer
ComponentsNuclear factor NF-kappa-B p100 subunit
KeywordsTRANSCRIPTION / NF-kB protein / p52 homodimer / dimerization domain / Activator / ANK repeat / DNA-binding / Isopeptide bond / Nucleus / Phosphoprotein / Transcription regulation
Function / homology
Function and homology information


follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / SUMOylation of immune response proteins / 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 / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / PKMTs methylate histone lysines ...follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / SUMOylation of immune response proteins / 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 / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / PKMTs methylate histone lysines / TAK1-dependent IKK and NF-kappa-B activation / germinal center formation / non-canonical NF-kappaB signal transduction / canonical NF-kappaB signal transduction / lymph node development / spleen development / extracellular matrix organization / response to cytokine / 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 / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear factor NF-kappa-B, p100 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. ...Nuclear factor NF-kappa-B, p100 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 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
Nuclear factor NF-kappa-B p100 subunit
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsVu, D. / Huang, D.B. / Ghosh, G.
CitationJournal: To be Published
Title: Instability of the RelB dimerization domain is functionally important
Authors: Vu, D. / Huang, D.B. / Ghosh, G.
History
DepositionSep 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 p100 subunit
B: Nuclear factor NF-kappa-B p100 subunit
C: Nuclear factor NF-kappa-B p100 subunit
D: Nuclear factor NF-kappa-B p100 subunit


Theoretical massNumber of molelcules
Total (without water)48,4074
Polymers48,4074
Non-polymers00
Water3,297183
1
A: Nuclear factor NF-kappa-B p100 subunit
B: Nuclear factor NF-kappa-B p100 subunit


Theoretical massNumber of molelcules
Total (without water)24,2032
Polymers24,2032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-5 kcal/mol
Surface area11200 Å2
MethodPISA
2
C: Nuclear factor NF-kappa-B p100 subunit
D: Nuclear factor NF-kappa-B p100 subunit


Theoretical massNumber of molelcules
Total (without water)24,2032
Polymers24,2032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-4 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.433, 56.863, 102.192
Angle α, β, γ (deg.)90.000, 97.770, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nuclear factor NF-kappa-B p100 subunit / DNA-binding factor KBF2 / Nuclear factor NF-kappa-B p52 subunit


Mass: 12101.670 Da / Num. of mol.: 4 / Fragment: dimerization domain (UNP residues 225-328)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: p52 / Plasmid: PET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9WTK5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 106 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 2, 2007 / Details: mirrors
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. all: 14659 / Num. obs: 13577 / % possible obs: 88 % / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 28.6 Å2 / Rsym value: 0.99 / Net I/σ(I): 10.1
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2 / Num. unique all: 1024 / Rsym value: 0.41 / % possible all: 64

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→19.71 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.808 / Data cutoff high absF: 363383 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 830 7 %RANDOM
Rwork0.209 ---
all-13550 --
obs-11799 75.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.85 Å2 / ksol: 0.311 e/Å3
Displacement parametersBiso max: 139.93 Å2 / Biso mean: 44.664 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--6.6 Å20 Å2-2.27 Å2
2--4.93 Å20 Å2
3---1.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.65→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3379 0 0 183 3562
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d1.01
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.409 72 7.3 %
Rwork0.378 911 -
all-983 -
obs--38 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2&_1_PARAMETER_INFILE_2&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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