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- PDB-6nv2: 14-3-3 sigma with RelA/p65 binding site pS45 in complex with DP005 -

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Basic information

Entry
Database: PDB / ID: 6nv2
Title14-3-3 sigma with RelA/p65 binding site pS45 in complex with DP005
Components
  • 14-3-3 protein sigma
  • Transcription factor p65
KeywordsPEPTIDE BINDING PROTEIN / fusicoccanes / natural products / p65 / 1433
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 / toll-like receptor TLR6:TLR2 signaling pathway / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / response to cobalamin / cellular response to peptidoglycan / ankyrin repeat binding / Regulated proteolysis of p75NTR ...prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / toll-like receptor TLR6:TLR2 signaling pathway / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / response to cobalamin / cellular response to peptidoglycan / ankyrin repeat binding / Regulated proteolysis of p75NTR / CLEC7A/inflammasome pathway / SUMOylation of immune response proteins / RIP-mediated NFkB activation via ZBP1 / Interleukin-1 processing / negative regulation of protein sumoylation / postsynapse to nucleus signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / defense response to tumor cell / cellular response to interleukin-6 / actinin binding / response to UV-B / non-canonical NF-kappaB signal transduction / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of miRNA metabolic process / positive regulation of leukocyte adhesion to vascular endothelial cell / Regulation of NFE2L2 gene expression / interleukin-1-mediated signaling pathway / NF-kappaB complex / signal transduction involved in regulation of gene expression / vascular endothelial growth factor signaling pathway / toll-like receptor 4 signaling pathway / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / phosphate ion binding / positive regulation of T cell receptor signaling pathway / cellular response to lipoteichoic acid / regulation of cell-cell adhesion / response to muramyl dipeptide / TRAF6 mediated NF-kB activation / positive regulation of vascular endothelial growth factor production / Transcriptional Regulation by VENTX / cellular response to angiotensin / The NLRP3 inflammasome / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / general transcription initiation factor binding / keratinocyte proliferation / cellular response to interleukin-1 / response to cAMP / canonical NF-kappaB signal transduction / Activation of BAD and translocation to mitochondria / hair follicle development / phosphoserine residue binding / negative regulation of keratinocyte proliferation / NF-kappaB binding / establishment of skin barrier / neuropeptide signaling pathway / response to amino acid / negative regulation of protein localization to plasma membrane / cellular defense response / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Purinergic signaling in leishmaniasis infection / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / response to muscle stretch / response to cytokine / positive regulation of interleukin-12 production / antiviral innate immune response / negative regulation of cytokine production involved in inflammatory response / peptide binding / CD209 (DC-SIGN) signaling / positive regulation of cell adhesion / negative regulation of insulin receptor signaling pathway / NF-kB is activated and signals survival / response to interleukin-1 / protein sequestering activity / protein export from nucleus / response to progesterone / negative regulation of innate immune response / negative regulation of miRNA transcription / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / negative regulation of angiogenesis / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / animal organ morphogenesis / positive regulation of protein export from nucleus / response to ischemia / positive regulation of interleukin-1 beta production / tumor necrosis factor-mediated signaling pathway / stem cell proliferation
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-0V4 / 14-3-3 protein sigma / Transcription factor p65
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsWolter, M. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European Commission 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
DepositionFeb 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 1, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.4Jan 24, 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 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)28,5034
Polymers27,9712
Non-polymers5322
Water6,071337
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)57,0078
Polymers55,9434
Non-polymers1,0644
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5270 Å2
ΔGint-44 kcal/mol
Surface area23210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.150, 112.070, 62.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 26558.914 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


Mass: 1412.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q04206*PLUS
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Sugar ChemComp-0V4 / (4R,5R,6R,6aS,9S,9aE,10aR)-5-hydroxy-9-(methoxymethyl)-6,10a-dimethyl-3-(propan-2-yl)-1,2,4,5,6,6a,7,8,9,10a-decahydrodicyclopenta[a,d][8]annulen-4-yl alpha-D-glucopyranoside / 16-O-Me-Fusicoccin H


Type: D-saccharide / Mass: 496.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C27H44O8
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.57 Å3/Da / Density % sol: 52.17 %
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: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.13→45.47 Å / Num. obs: 352244 / % possible obs: 98.9 % / Redundancy: 3.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.029 / Rrim(I) all: 0.054 / Net I/σ(I): 15.1
Reflection shellResolution: 1.13→1.15 Å / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 4.4 / CC1/2: 0.929 / Rrim(I) all: 0.258 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MHR

3mhr


Resolution: 1.13→45.468 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.51
RfactorNum. reflection% reflection
Rfree0.1795 5405 5.04 %
Rwork0.1605 --
obs0.1614 107181 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.13→45.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1908 0 36 337 2281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112003
X-RAY DIFFRACTIONf_angle_d1.3952707
X-RAY DIFFRACTIONf_dihedral_angle_d19.55756
X-RAY DIFFRACTIONf_chiral_restr0.092300
X-RAY DIFFRACTIONf_plane_restr0.007349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.127-1.13980.23261830.21553375X-RAY DIFFRACTION99
1.1398-1.15320.21521850.20113357X-RAY DIFFRACTION99
1.1532-1.16730.22081810.2073323X-RAY DIFFRACTION98
1.1673-1.18210.2211860.19333384X-RAY DIFFRACTION99
1.1821-1.19760.23991760.1863384X-RAY DIFFRACTION99
1.1976-1.2140.21991960.17893295X-RAY DIFFRACTION99
1.214-1.23140.19481890.17783336X-RAY DIFFRACTION98
1.2314-1.24980.18641770.16143366X-RAY DIFFRACTION99
1.2498-1.26930.17981830.15633387X-RAY DIFFRACTION99
1.2693-1.29010.16531560.14923370X-RAY DIFFRACTION98
1.2901-1.31230.1551760.14513378X-RAY DIFFRACTION98
1.3123-1.33620.17181680.14893392X-RAY DIFFRACTION99
1.3362-1.36190.19591810.15243354X-RAY DIFFRACTION99
1.3619-1.38970.17641550.14663397X-RAY DIFFRACTION98
1.3897-1.41990.15361570.13773344X-RAY DIFFRACTION97
1.4199-1.4530.15281640.13083390X-RAY DIFFRACTION99
1.453-1.48930.15841680.12523404X-RAY DIFFRACTION99
1.4893-1.52960.14091900.12133361X-RAY DIFFRACTION99
1.5296-1.57460.13191900.12553361X-RAY DIFFRACTION98
1.5746-1.62540.15572010.12813381X-RAY DIFFRACTION99
1.6254-1.68350.16851870.13353359X-RAY DIFFRACTION98
1.6835-1.75090.16741890.14193378X-RAY DIFFRACTION98
1.7509-1.83060.14911650.15713434X-RAY DIFFRACTION99
1.8306-1.92710.16441720.16443398X-RAY DIFFRACTION99
1.9271-2.04790.17911830.16173411X-RAY DIFFRACTION99
2.0479-2.2060.17391800.14593424X-RAY DIFFRACTION99
2.206-2.4280.16351930.14853432X-RAY DIFFRACTION99
2.428-2.77930.16651790.16633493X-RAY DIFFRACTION99
2.7793-3.50140.19621860.17393482X-RAY DIFFRACTION99
3.5014-45.50490.20812090.1883626X-RAY DIFFRACTION99

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