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- PDB-9bor: IkappaBzeta ankyrin repeat domain:NF-kappaB p50 homodimer complex... -

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Basic information

Entry
Database: PDB / ID: 9bor
TitleIkappaBzeta ankyrin repeat domain:NF-kappaB p50 homodimer complex at 2.0 Angstrom resolution
Components
  • NF-kappa-B inhibitor zeta
  • Nuclear factor NF-kappa-B p50 subunit
KeywordsTRANSCRIPTION / Transcription factor / immunoglobulin-like domain / ankyrin repeat domain / protein-protein complex / NF-kappaB / IkappaB
Function / homology
Function and homology information


keratinocyte activation / response to cisplatin / positive regulation of T-helper 17 cell differentiation / Regulated proteolysis of p75NTR / I-kappaB/NF-kappaB complex / B cell receptor apoptotic signaling pathway / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / chronic inflammatory response / transcription preinitiation complex assembly ...keratinocyte activation / response to cisplatin / positive regulation of T-helper 17 cell differentiation / Regulated proteolysis of p75NTR / I-kappaB/NF-kappaB complex / B cell receptor apoptotic signaling pathway / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / chronic inflammatory response / transcription preinitiation complex assembly / RIP-mediated NFkB activation via ZBP1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / T-helper 1 cell differentiation / TRAF6 mediated NF-kB activation / positive regulation of hyaluronan biosynthetic process / response to Gram-positive bacterium / NF-kB is activated and signals survival / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / T cell mediated immunity / TAK1-dependent IKK and NF-kappa-B activation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / mammary gland involution / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / POU domain binding / Interleukin-1 signaling / antibacterial innate immune response / Downstream TCR signaling / cellular response to interleukin-17 / inflammatory response to wounding / NF-kappaB p50/p65 complex / T-helper 17 cell differentiation / CD209 (DC-SIGN) signaling / positive regulation of lipid storage / negative regulation of interleukin-12 production / cellular response to interleukin-6 / response to folic acid / isotype switching / plasma cell differentiation / cellular response to dsRNA / actinin binding / positive regulation of macrophage derived foam cell differentiation / non-canonical NF-kappaB signal transduction / positive regulation of miRNA metabolic process / epithelial cell apoptotic process / negative regulation of cytokine production / execution phase of apoptosis / toll-like receptor signaling pathway / cellular response to cytokine stimulus / : / B cell proliferation / keratinocyte proliferation / cellular response to interleukin-1 / cellular response to angiotensin / positive regulation of cholesterol efflux / canonical NF-kappaB signal transduction / positive regulation of transcription initiation by RNA polymerase II / establishment of skin barrier / lymph node development / keratinocyte differentiation / cellular response to transforming growth factor beta stimulus / spleen development / JNK cascade / homeostasis of number of cells within a tissue / response to muscle stretch / Neutrophil degranulation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / B cell receptor signaling pathway / transcription coregulator activity / mRNA transcription by RNA polymerase II / cytokine-mediated signaling pathway / cellular response to virus / DNA-binding transcription repressor activity, RNA polymerase II-specific / cellular response to nicotine / negative regulation of inflammatory response / cytoplasmic ribonucleoprotein granule / cellular response to mechanical stimulus / positive regulation of inflammatory response / positive regulation of canonical Wnt signaling pathway / MAPK cascade / cellular response to tumor necrosis factor / T cell receptor signaling pathway / regulation of gene expression / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / defense response to Gram-negative bacterium / gene expression / transcription regulator complex / sequence-specific DNA binding / transcription cis-regulatory region binding / nuclear speck / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / apoptotic process / chromatin binding / chromatin
Similarity search - Function
: / OCA domain profile. / 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 ...: / OCA domain profile. / 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
Similarity search - Domain/homology
(2R,3S)-heptane-1,2,3-triol / Nuclear factor NF-kappa-B p105 subunit / NF-kappa-B inhibitor zeta
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 Å
AuthorsRogers, W.E. / Zhu, N. / Huxford, T.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Genes Dev. / Year: 2024
Title: Structural and biochemical analyses of the nuclear I kappa B zeta protein in complex with the NF-kappa B p50 homodimer.
Authors: Zhu, N. / Rogers, W.E. / Heidary, D.K. / Huxford, T.
History
DepositionMay 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NF-kappa-B inhibitor zeta
B: Nuclear factor NF-kappa-B p50 subunit
C: Nuclear factor NF-kappa-B p50 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3764
Polymers65,2283
Non-polymers1481
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-12 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.415, 58.931, 108.806
Angle α, β, γ (deg.)90.00, 99.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NF-kappa-B inhibitor zeta / I-kappa-B-zeta / IkB-zeta / IkappaBzeta / IL-1 inducible nuclear ankyrin-repeat protein / INAP / ...I-kappa-B-zeta / IkB-zeta / IkappaBzeta / IL-1 inducible nuclear ankyrin-repeat protein / INAP / Molecule possessing ankyrin repeats induced by lipopolysaccharide / MAIL


Mass: 34773.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFKBIZ, IKBZ, INAP, MAIL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BYH8
#2: Protein Nuclear factor NF-kappa-B p50 subunit


Mass: 15227.196 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C and N terminus unstable and not modeled / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nfkb1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25799
#3: Chemical ChemComp-HT3 / (2R,3S)-heptane-1,2,3-triol


Mass: 148.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop
Details: 20mM acetic acid pH 5.2, 80mM acetic acid pH 5.8, 5.5% PEG 3350, 10mM DTT, 0.5% 1,2,3 heptanetriol
PH range: 5.2-5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.997→50 Å / Num. all: 43896 / Num. obs: 43393 / % possible obs: 98.89 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rsym value: 0.055 / Net I/σ(I): 20.4
Reflection shellResolution: 1.997→2.041 Å / Mean I/σ(I) obs: 2.097 / Num. unique obs: 2608 / Rsym value: 0.468 / % possible all: 96.51

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TRV

4trv
PDB Unreleased entry


Resolution: 1.997→43.31 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 2184 5.04 %Random selection
Rwork0.1809 ---
obs0.1823 43365 98.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.93 Å2
Refinement stepCycle: LAST / Resolution: 1.997→43.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4147 0 10 318 4475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054233
X-RAY DIFFRACTIONf_angle_d0.9145718
X-RAY DIFFRACTIONf_dihedral_angle_d14.0071597
X-RAY DIFFRACTIONf_chiral_restr0.041638
X-RAY DIFFRACTIONf_plane_restr0.004749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.997-2.04090.31321310.24182477X-RAY DIFFRACTION96
2.0409-2.08840.26051130.23772526X-RAY DIFFRACTION98
2.0884-2.14060.26961310.22532560X-RAY DIFFRACTION98
2.1406-2.19850.26711410.20932513X-RAY DIFFRACTION98
2.1985-2.26320.26861370.21352539X-RAY DIFFRACTION98
2.2632-2.33620.24871290.20312558X-RAY DIFFRACTION98
2.3362-2.41970.24871400.2082542X-RAY DIFFRACTION99
2.4197-2.51660.24711670.20682534X-RAY DIFFRACTION99
2.5166-2.63110.23981380.19582577X-RAY DIFFRACTION100
2.6311-2.76980.2281280.20052598X-RAY DIFFRACTION100
2.7698-2.94330.22351180.19622617X-RAY DIFFRACTION100
2.9433-3.17050.22611490.18812594X-RAY DIFFRACTION100
3.1705-3.48940.19051320.17542608X-RAY DIFFRACTION100
3.4894-3.9940.19751330.16562635X-RAY DIFFRACTION100
3.994-5.03090.15841420.14632620X-RAY DIFFRACTION100
5.0309-43.310.17881550.16292683X-RAY DIFFRACTION100

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