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- PDB-7nk3: 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound... -

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Basic information

Entry
Database: PDB / ID: 7nk3
Title14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-128
Components
  • 14-3-3 protein sigma
  • Transcription factor p65
KeywordsPEPTIDE BINDING PROTEIN / benzaldehyde / covalent fragment / p65 / 1433 / RelA
Function / homology
Function and homology information


toll-like receptor TLR6:TLR2 signaling pathway / acetaldehyde metabolic process / 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 / positive regulation of Schwann cell differentiation / cellular response to peptidoglycan / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 ...toll-like receptor TLR6:TLR2 signaling pathway / acetaldehyde metabolic process / 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 / positive regulation of Schwann cell differentiation / cellular response to peptidoglycan / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / Regulated proteolysis of p75NTR / SUMOylation of immune response proteins / CLEC7A/inflammasome pathway / negative regulation of protein sumoylation / postsynapse to nucleus signaling pathway / defense response to tumor cell / cellular response to interleukin-6 / Interleukin-1 processing / nucleotide-binding oligomerization domain containing 2 signaling pathway / actinin binding / cellular response to angiotensin / negative regulation of non-canonical NF-kappaB signal transduction / response to UV-B / NF-kappaB complex / positive regulation of leukocyte adhesion to vascular endothelial cell / interleukin-1-mediated signaling pathway / Regulation of NFE2L2 gene expression / positive regulation of miRNA metabolic process / vascular endothelial growth factor signaling pathway / non-canonical NF-kappaB signal transduction / toll-like receptor 4 signaling pathway / positive regulation of amyloid-beta formation / cellular response to hepatocyte growth factor stimulus / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / response to cobalamin / keratinization / positive regulation of T cell receptor signaling pathway / phosphate ion binding / regulation of cell-cell adhesion / cellular response to lipoteichoic acid / response to muramyl dipeptide / TRAF6 mediated NF-kB activation / The NLRP3 inflammasome / Regulation of localization of FOXO transcription factors / general transcription initiation factor binding / keratinocyte proliferation / Transcriptional Regulation by VENTX / neuropeptide signaling pathway / cellular response to interleukin-1 / phosphoserine residue binding / NF-kappaB binding / hair follicle development / positive regulation of vascular endothelial growth factor production / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / response to amino acid / RNA polymerase II core promoter sequence-specific DNA binding / establishment of skin barrier / negative regulation of protein localization to plasma membrane / cellular defense response / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Purinergic signaling in leishmaniasis infection / canonical NF-kappaB signal transduction / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / RHO GTPases activate PKNs / antiviral innate immune response / negative regulation of insulin receptor signaling pathway / tumor necrosis factor-mediated signaling pathway / response to cAMP / response to muscle stretch / protein kinase A signaling / protein sequestering activity / positive regulation of interleukin-12 production / protein export from nucleus / negative regulation of innate immune response / CD209 (DC-SIGN) signaling / positive regulation of cell adhesion / NF-kB is activated and signals survival / response to interleukin-1 / negative regulation of angiogenesis / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / negative regulation of miRNA transcription / positive regulation of protein export from nucleus / liver development / stem cell proliferation / response to cytokine / positive regulation of interleukin-1 beta production / response to ischemia / positive regulation of interleukin-8 production / response to progesterone / Translocation of SLC2A4 (GLUT4) to the plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / TP53 Regulates Metabolic Genes
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 / ig-like, plexins, transcription factors / IPT domain / 14-3-3 protein sigma / 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 / p53-like transcription factor, DNA-binding / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-UGQ / 14-3-3 protein sigma / Transcription factor p65
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsWolter, M. / Ottmann, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission675179European Union
CitationJournal: J.Med.Chem. / Year: 2021
Title: An Exploration of Chemical Properties Required for Cooperative Stabilization of the 14-3-3 Interaction with NF-kappa B-Utilizing a Reversible Covalent Tethering Approach.
Authors: Wolter, M. / Valenti, D. / Cossar, P.J. / Hristeva, S. / Levy, L.M. / Genski, T. / Hoffmann, T. / Brunsveld, L. / Tzalis, D. / Ottmann, C.
History
DepositionFeb 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)30,0946
Polymers29,6392
Non-polymers4554
Water5,423301
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)60,18812
Polymers59,2784
Non-polymers9108
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5280 Å2
ΔGint-36 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.712, 112.424, 62.726
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-303-

CA

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AP

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


Mass: 28226.518 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: 1412.429 Da / Num. of mol.: 1 / Mutation: R49E / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q04206

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Non-polymers , 5 types, 305 molecules

#3: Chemical ChemComp-UGQ / 2-(4-methylphenyl)sulfonyl-3,4-dihydro-1~{H}-isoquinoline


Mass: 287.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.46 Å3/Da / Density % sol: 50 % / Mosaicity: 0 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.095 M HEPES Na pH 7.1, 27% 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: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.4→45.67 Å / Num. obs: 57817 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 12.86 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.053 / Rrim(I) all: 0.19 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.4-1.4212.60.5693585228460.9270.1660.5944.2100
7.67-45.6711.70.17648044120.9820.0520.18413.799.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
MOLREPphasing
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QHL

6qhl


Resolution: 1.4→41.86 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.13 / Stereochemistry target values: ML / Details: MOLECULAR REPLACEMENT
RfactorNum. reflection% reflection
Rfree0.1927 2927 5.04 %
Rwork0.1725 105674 -
obs0.1735 57788 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.3 Å2 / Biso mean: 18.0886 Å2 / Biso min: 7.27 Å2
Refinement stepCycle: final / Resolution: 1.4→41.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 28 301 2165
Biso mean--31.24 28.55 -
Num. residues----236
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.4-1.420.29521560.229435053661
1.42-1.430.23141860.233135113697
1.43-1.450.22811590.215235853744
1.45-1.470.26531960.201435063702
1.47-1.490.20322180.197235453763
1.49-1.510.24231710.192934953666
1.51-1.530.20911870.183435513738
1.53-1.550.22091880.181835013689
1.55-1.580.18982240.182234723696
1.58-1.60.19831710.179134953666
1.6-1.630.2162020.176935353737
1.63-1.660.2121950.179335403735
1.66-1.690.20212050.177434653670
1.69-1.730.23061800.185735493729
1.73-1.760.20492160.183835083724
1.76-1.80.22111630.182935523715
1.8-1.850.18342050.179434973702
1.85-1.90.20361680.178535113679
1.9-1.960.18532080.171635493757
1.96-2.020.19251860.170435063692
2.02-2.090.16711880.163935323720
2.09-2.170.16132110.158634993710
2.18-2.270.16651880.156535103698
2.27-2.390.16132160.156234913707
2.39-2.540.19521770.167335363713
2.54-2.740.18111600.17535393699
2.74-3.020.21032010.175135303731
3.02-3.450.17811550.168935473702
3.45-4.350.16561590.154235603719
4.35-41.860.21731660.176335523718

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