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- PDB-6qhm: 14-3-3 sigma with RelA/p65 binding site pS281 -

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Basic information

Entry
Database: PDB / ID: 6qhm
Title14-3-3 sigma with RelA/p65 binding site pS281
Components
  • 14-3-3 protein sigma
  • LEU-SEP-GLU
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 / 14-3-3 sigma / p65 / RelA
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 / cellular response to peptidoglycan / Regulated proteolysis of p75NTR / ankyrin repeat binding / SUMOylation of immune response proteins ...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 / cellular response to peptidoglycan / Regulated proteolysis of p75NTR / ankyrin repeat binding / SUMOylation of immune response proteins / CLEC7A/inflammasome pathway / RIP-mediated NFkB activation via ZBP1 / postsynapse to nucleus signaling pathway / negative regulation of protein sumoylation / Interleukin-1 processing / defense response to tumor cell / cellular response to interleukin-6 / nucleotide-binding oligomerization domain containing 2 signaling pathway / actinin binding / response to UV-B / negative regulation of non-canonical NF-kappaB signal transduction / signal transduction involved in regulation of gene expression / 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 / vascular endothelial growth factor signaling pathway / 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 / keratinization / response to cobalamin / phosphate ion binding / positive regulation of T cell receptor signaling pathway / regulation of cell-cell adhesion / cellular response to lipoteichoic acid / response to muramyl dipeptide / TRAF6 mediated NF-kB activation / cAMP/PKA signal transduction / The NLRP3 inflammasome / Transcriptional Regulation by VENTX / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / cellular response to interleukin-1 / general transcription initiation factor binding / cellular response to angiotensin / positive regulation of vascular endothelial growth factor production / phosphoserine residue binding / canonical NF-kappaB signal transduction / hair follicle development / Activation of BAD and translocation to mitochondria / response to amino acid / negative regulation of keratinocyte proliferation / neuropeptide signaling pathway / establishment of skin barrier / NF-kappaB binding / 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 stem cell proliferation / response to cAMP / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / tumor necrosis factor-mediated signaling pathway / positive regulation of protein localization / response to muscle stretch / antiviral innate immune response / positive regulation of interleukin-12 production / negative regulation of cytokine production involved in inflammatory response / CD209 (DC-SIGN) signaling / negative regulation of insulin receptor signaling pathway / response to cytokine / positive regulation of cell adhesion / response to interleukin-1 / negative regulation of miRNA transcription / NF-kB is activated and signals survival / peptide binding / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of angiogenesis / liver development / response to progesterone / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / positive regulation of interleukin-1 beta production / positive regulation of protein export from nucleus / response to ischemia / animal organ morphogenesis / negative regulation of protein kinase activity
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
14-3-3 protein sigma / Transcription factor p65
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 1.1Jun 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 1.5Oct 23, 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: LEU-SEP-GLU


Theoretical massNumber of molelcules
Total (without water)29,8722
Polymers29,8722
Non-polymers00
Water6,395355
1
A: 14-3-3 protein sigma
P: LEU-SEP-GLU

A: 14-3-3 protein sigma
P: LEU-SEP-GLU


Theoretical massNumber of molelcules
Total (without water)59,7444
Polymers59,7444
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3130 Å2
ΔGint-20 kcal/mol
Surface area23350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.500, 111.940, 62.570
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: 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 LEU-SEP-GLU


Mass: 1645.659 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q04206*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
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: 1.03322 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: 1.03322 Å / Relative weight: 1
ReflectionResolution: 1.25→62.57 Å / Num. obs: 80102 / % possible obs: 99.9 % / Redundancy: 8.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.079 / Net I/σ(I): 15.2
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.744 / Num. unique obs: 4152 / CC1/2: 0.723 / Rrim(I) all: 0.88 / % possible all: 99

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Processing

Software
NameClassification
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MHR

3mhr


Resolution: 1.25→55.97 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.69
RfactorNum. reflection% reflection
Rfree0.16 4076 5.09 %
Rwork0.136 --
obs0.1372 80068 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.25→55.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 0 355 2207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072007
X-RAY DIFFRACTIONf_angle_d0.8762726
X-RAY DIFFRACTIONf_dihedral_angle_d19.321767
X-RAY DIFFRACTIONf_chiral_restr0.061298
X-RAY DIFFRACTIONf_plane_restr0.006365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.26470.22741230.222560X-RAY DIFFRACTION98
1.2647-1.28010.20761370.20282597X-RAY DIFFRACTION100
1.2801-1.29630.20581450.18432573X-RAY DIFFRACTION100
1.2963-1.31340.19251400.18182604X-RAY DIFFRACTION100
1.3134-1.33140.20861530.18332586X-RAY DIFFRACTION100
1.3314-1.35040.21371620.17852570X-RAY DIFFRACTION100
1.3504-1.37060.17341350.16852571X-RAY DIFFRACTION100
1.3706-1.3920.20561400.15952634X-RAY DIFFRACTION100
1.392-1.41480.17731330.14892610X-RAY DIFFRACTION100
1.4148-1.43920.17251480.132594X-RAY DIFFRACTION100
1.4392-1.46540.13441470.11822572X-RAY DIFFRACTION100
1.4654-1.49360.12981430.11492612X-RAY DIFFRACTION100
1.4936-1.52410.13771470.10852617X-RAY DIFFRACTION100
1.5241-1.55720.15581440.112614X-RAY DIFFRACTION100
1.5572-1.59340.11741410.10532568X-RAY DIFFRACTION100
1.5934-1.63330.11691360.10362599X-RAY DIFFRACTION100
1.6333-1.67740.14571310.10482628X-RAY DIFFRACTION100
1.6774-1.72680.14871430.1122626X-RAY DIFFRACTION100
1.7268-1.78250.1361470.1152626X-RAY DIFFRACTION100
1.7825-1.84630.14871360.11772600X-RAY DIFFRACTION100
1.8463-1.92020.1331290.11692645X-RAY DIFFRACTION100
1.9202-2.00760.14431260.12562634X-RAY DIFFRACTION100
2.0076-2.11340.15551200.11872668X-RAY DIFFRACTION100
2.1134-2.24580.14581340.11852654X-RAY DIFFRACTION100
2.2458-2.41920.12591440.12272627X-RAY DIFFRACTION100
2.4192-2.66270.1561530.132653X-RAY DIFFRACTION100
2.6627-3.0480.18161560.14762644X-RAY DIFFRACTION100
3.048-3.840.15421410.13932693X-RAY DIFFRACTION100
3.84-56.02620.19661420.16562813X-RAY DIFFRACTION100

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