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- PDB-6qhl: 14-3-3 sigma with RelA/p65 binding site pS45 -

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Basic information

Entry
Database: PDB / ID: 6qhl
Title14-3-3 sigma with RelA/p65 binding site pS45
Components
  • 14-3-3 protein sigma
  • Transcription factor p65
KeywordsSIGNALING PROTEIN / 14-3-3 / p65
Function / homology
Function and homology information


prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / toll-like receptor TLR6:TLR2 signaling pathway / cellular response to peptidoglycan / Regulated proteolysis of p75NTR / nucleotide-binding oligomerization domain containing 2 signaling pathway / SUMOylation of immune response proteins / CLEC7A/inflammasome pathway ...prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / toll-like receptor TLR6:TLR2 signaling pathway / cellular response to peptidoglycan / Regulated proteolysis of p75NTR / nucleotide-binding oligomerization domain containing 2 signaling pathway / SUMOylation of immune response proteins / CLEC7A/inflammasome pathway / RIP-mediated NFkB activation via ZBP1 / ankyrin repeat binding / negative regulation of protein sumoylation / Interleukin-1 processing / postsynapse to nucleus signaling pathway / defense response to tumor cell / response to UV-B / cellular response to interleukin-6 / actinin binding / negative regulation of non-canonical NF-kappaB signal transduction / Regulation of NFE2L2 gene expression / positive regulation of miRNA metabolic process / positive regulation of leukocyte adhesion to vascular endothelial cell / interleukin-1-mediated signaling pathway / toll-like receptor 4 signaling pathway / positive regulation of cytokine production involved in inflammatory response / non-canonical NF-kappaB signal transduction / positive regulation of amyloid-beta formation / vascular endothelial growth factor signaling pathway / cGAS/STING signaling pathway / NF-kappaB complex / positive regulation of epidermal cell differentiation / cellular response to lipoteichoic acid / regulation of epidermal cell division / protein kinase C inhibitor activity / phosphate ion binding / regulation of cell-cell adhesion / TRAF6 mediated NF-kB activation / cellular response to angiotensin / Transcriptional Regulation by VENTX / establishment of skin barrier / Regulation of localization of FOXO transcription factors / cellular response to interleukin-1 / Regulation of GBP-mediated host defense / The NLRP3 inflammasome / positive regulation of vascular endothelial growth factor production / Activation of BAD and translocation to mitochondria / general transcription initiation factor binding / phosphoserine residue binding / negative regulation of protein localization to plasma membrane / cAMP/PKA signal transduction / NF-kappaB binding / protein export from nucleus / RNA polymerase II core promoter sequence-specific DNA binding / cellular defense response / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Purinergic signaling in leishmaniasis infection / release of cytochrome c from mitochondria / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / canonical NF-kappaB signal transduction / positive regulation of protein export from nucleus / positive regulation of protein localization / response to cytokine / peptide binding / negative regulation of angiogenesis / negative regulation of cytokine production involved in inflammatory response / CD209 (DC-SIGN) signaling / negative regulation of miRNA transcription / liver development / positive regulation of cell adhesion / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of innate immune response / response to interleukin-1 / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / negative regulation of extrinsic apoptotic signaling pathway / NF-kB is activated and signals survival / tumor necrosis factor-mediated signaling pathway / antiviral innate immune response / positive regulation of interleukin-8 production / positive regulation of interleukin-1 beta production / TP53 Regulates Metabolic Genes / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cellular response to tumor necrosis factor / intrinsic apoptotic signaling pathway in response to DNA damage / Translocation of SLC2A4 (GLUT4) to the plasma membrane / neuropeptide signaling pathway / Dectin-1 mediated noncanonical NF-kB signaling / protein sequestering activity / Transcriptional regulation of white adipocyte differentiation / chromatin DNA binding / Activation of NF-kappaB in B cells / positive regulation of interleukin-6 production / cellular response to nicotine / positive regulation of miRNA transcription / TAK1-dependent IKK and NF-kappa-B activation / DNA-binding transcription repressor activity, RNA polymerase II-specific / PKMTs methylate histone lysines
Similarity search - Function
Transcription factor RelA (p65) / 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. ...Transcription factor RelA (p65) / 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 / 14-3-3 domain / ig-like, plexins, transcription factors / Delta-Endotoxin; domain 1 / IPT domain / 14-3-3 protein sigma / p53-like transcription factor, DNA-binding / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Immunoglobulin E-set / Immunoglobulin-like fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein sigma / Transcription factor p65
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å
AuthorsWolter, M. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European CommissionH2020 Marie Curie Actions, Grant Agreement 675179 Netherlands
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Selectivity via Cooperativity: Preferential Stabilization of the p65/14-3-3 Interaction with Semisynthetic Natural Products.
Authors: Wolter, M. / de Vink, P. / Neves, J.F. / Srdanovic, S. / Higuchi, Y. / Kato, N. / Wilson, A. / Landrieu, I. / Brunsveld, L. / Ottmann, C.
History
DepositionJan 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: 14-3-3 protein sigma
P: Transcription factor p65
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8784
Polymers29,6942
Non-polymers1842
Water7,800433
1
A: 14-3-3 protein sigma
P: Transcription factor p65
hetero molecules

A: 14-3-3 protein sigma
P: Transcription factor p65
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7568
Polymers59,3884
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5330 Å2
ΔGint-23 kcal/mol
Surface area23700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.340, 112.390, 62.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-410-

HOH

21A-775-

HOH

31A-810-

HOH

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Components

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 28210.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide Transcription factor p65 / Nuclear factor NF-kappa-B p65 subunit / Nuclear factor of kappa light polypeptide gene enhancer in B-cells 3


Mass: 1483.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RELA, NFKB3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04206
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.095 M HEPES Na pH 7.1, 28% PEG400, 0.19M Calcium chloride, 5% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9919 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 1.2→62.61 Å / Num. obs: 90213 / % possible obs: 99.4 % / Redundancy: 11.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.078 / Net I/σ(I): 18.1
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.391 / Num. unique obs: 4101 / CC1/2: 0.9 / Rrim(I) all: 0.438 / % possible all: 92.5

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Processing

Software
NameClassification
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 1.2→56.195 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.19
RfactorNum. reflection% reflection
Rfree0.1644 4562 5.06 %
Rwork0.15 --
obs0.1507 90176 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.2→56.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1901 0 12 433 2346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112082
X-RAY DIFFRACTIONf_angle_d1.0582830
X-RAY DIFFRACTIONf_dihedral_angle_d16.965818
X-RAY DIFFRACTIONf_chiral_restr0.073310
X-RAY DIFFRACTIONf_plane_restr0.007376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.21360.21621490.20922594X-RAY DIFFRACTION91
1.2136-1.22790.20631660.19112660X-RAY DIFFRACTION95
1.2279-1.24290.21191310.18182775X-RAY DIFFRACTION98
1.2429-1.25860.17761380.18192821X-RAY DIFFRACTION99
1.2586-1.27520.19011710.17112824X-RAY DIFFRACTION100
1.2752-1.29270.18051680.16822853X-RAY DIFFRACTION100
1.2927-1.31110.17081710.1652799X-RAY DIFFRACTION100
1.3111-1.33070.19851740.16262840X-RAY DIFFRACTION100
1.3307-1.35150.16181510.16352817X-RAY DIFFRACTION100
1.3515-1.37370.16751600.15932861X-RAY DIFFRACTION100
1.3737-1.39730.17631710.16212860X-RAY DIFFRACTION100
1.3973-1.42280.17121470.15832852X-RAY DIFFRACTION100
1.4228-1.45010.16531580.15152832X-RAY DIFFRACTION100
1.4501-1.47970.15911640.14922841X-RAY DIFFRACTION100
1.4797-1.51190.15181510.14712849X-RAY DIFFRACTION100
1.5119-1.54710.17111580.14842848X-RAY DIFFRACTION100
1.5471-1.58580.16141410.14232870X-RAY DIFFRACTION100
1.5858-1.62860.13931430.13872867X-RAY DIFFRACTION100
1.6286-1.67660.14661520.13752870X-RAY DIFFRACTION100
1.6766-1.73070.14641470.13852868X-RAY DIFFRACTION100
1.7307-1.79260.18951470.14522884X-RAY DIFFRACTION100
1.7926-1.86430.15621430.1492877X-RAY DIFFRACTION100
1.8643-1.94920.16641410.14652897X-RAY DIFFRACTION100
1.9492-2.05190.17791310.14262893X-RAY DIFFRACTION100
2.0519-2.18050.14171430.13312906X-RAY DIFFRACTION100
2.1805-2.34890.14421340.1312912X-RAY DIFFRACTION100
2.3489-2.58530.15711590.13632903X-RAY DIFFRACTION100
2.5853-2.95930.16541460.14912916X-RAY DIFFRACTION100
2.9593-3.72830.15911440.14462961X-RAY DIFFRACTION100
3.7283-56.25670.171630.16763064X-RAY DIFFRACTION100

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