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- PDB-4ot9: crystal structure of the C-terminal domain of p100/NF-kB2 -

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Basic information

Entry
Database: PDB / ID: 4ot9
Titlecrystal structure of the C-terminal domain of p100/NF-kB2
ComponentsNuclear factor NF-kappa-B p100 subunit
KeywordsTRANSCRIPTION / NF-kB transcription factor
Function / homology
Function and homology information


follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / IkBA variant leads to EDA-ID / germinal center formation / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / Interleukin-1 processing / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation ...follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / IkBA variant leads to EDA-ID / germinal center formation / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / Interleukin-1 processing / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation / The NLRP3 inflammasome / canonical NF-kappaB signal transduction / Purinergic signaling in leishmaniasis infection / spleen development / extracellular matrix organization / response to cytokine / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / TAK1-dependent IKK and NF-kappa-B activation / PKMTs methylate histone lysines / sequence-specific double-stranded DNA binding / rhythmic process / 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 / chromatin / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol
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 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
Similarity search - Domain/homology
Nuclear factor NF-kappa-B p100 subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsTao, Z.H. / Huang, D.B. / Fusco, A. / Gupta, K. / Ware, C.F. / Duynne, G.V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: p100/I kappa B delta sequesters and inhibits NF-kappa B through kappaBsome formation.
Authors: Tao, Z. / Fusco, A. / Huang, D.B. / Gupta, K. / Young Kim, D. / Ware, C.F. / Van Duyne, G.D. / Ghosh, G.
History
DepositionFeb 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear factor NF-kappa-B p100 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4743
Polymers38,2821
Non-polymers1922
Water00
1
A: Nuclear factor NF-kappa-B p100 subunit
hetero molecules

A: Nuclear factor NF-kappa-B p100 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9496
Polymers76,5642
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
Buried area3760 Å2
ΔGint-77 kcal/mol
Surface area28640 Å2
MethodPISA
2
A: Nuclear factor NF-kappa-B p100 subunit
hetero molecules

A: Nuclear factor NF-kappa-B p100 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9496
Polymers76,5642
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
Buried area1970 Å2
ΔGint-60 kcal/mol
Surface area30430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.670, 196.670, 68.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Nuclear factor NF-kappa-B p100 subunit / DNA-binding factor KBF2 / H2TF1 / Lymphocyte translocation chromosome 10 protein / Nuclear factor ...DNA-binding factor KBF2 / H2TF1 / Lymphocyte translocation chromosome 10 protein / Nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 / Oncogene Lyt-10 / Lyt10 / Nuclear factor NF-kappa-B p52 subunit


Mass: 38282.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFKB2, LYT10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00653
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.99 Å3/Da / Density % sol: 75.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG 4000, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 170.81 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2011
RadiationMonochromator: Cryo-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.34→30 Å / Num. all: 11531 / Num. obs: 10842 / % possible obs: 92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.4 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 14.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
3.34-3.469.60.5940.59199
3.46-3.69.60.375.60.37199
3.6-3.769.60.277.20.27199
3.76-3.969.60.1790.121100
3.96-4.219.50.116100.09199
4.21-4.539.50.088110.09199
4.53-4.999.50.086120.09199
4.99-5.719.40.087150.09198
5.71-7.199.10.065200.07198
7.19-508.40.028300.03195

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Processing

Software
NameVersionClassification
HKL-3000data collection
MERLOTphasing
CNS1.3refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→29.57 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 61874.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.272 568 5.2 %RANDOM
Rwork0.233 ---
obs0.233 10842 92.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.6404 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 126.4 Å2
Baniso -1Baniso -2Baniso -3
1-15.14 Å20 Å20 Å2
2--15.14 Å20 Å2
3----30.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 3.35→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2214 0 10 0 2224
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it22.31.5
X-RAY DIFFRACTIONc_mcangle_it27.222
X-RAY DIFFRACTIONc_scbond_it36.132
X-RAY DIFFRACTIONc_scangle_it36.62.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 3.34→3.55 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 76 5.1 %
Rwork0.303 1406 -
obs--77.7 %
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
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6as.paramas.top

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