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- PDB-6ypy: 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound... -

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Basic information

Entry
Database: PDB / ID: 6ypy
Title14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-123
Components
  • 14-3-3 protein sigma
  • p65pS45
KeywordsPEPTIDE BINDING PROTEIN / covalent fragment / 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 / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / hair follicle development / neuropeptide signaling pathway / negative regulation of keratinocyte proliferation / NF-kappaB binding / establishment of skin barrier / 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 / RNA polymerase II core promoter sequence-specific DNA binding / Purinergic signaling in leishmaniasis infection / 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 / response to interleukin-1 / NF-kB is activated and signals survival / protein sequestering activity / response to progesterone / protein export from nucleus / negative regulation of miRNA transcription / negative regulation of innate immune response / 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
4-(4-ethanoylpiperazin-1-yl)sulfonylbenzaldehyde / 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
European Commission675179European Union
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Fragment-Based Stabilizers of Protein-Protein Interactions through Imine-Based Tethering.
Authors: Wolter, M. / Valenti, D. / Cossar, P.J. / Levy, L.M. / Hristeva, S. / Genski, T. / Hoffmann, T. / Brunsveld, L. / Tzalis, D. / Ottmann, C.
History
DepositionApr 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Dec 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 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 1.4Oct 16, 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: p65pS45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2683
Polymers27,9712
Non-polymers2961
Water5,999333
1
A: 14-3-3 protein sigma
P: p65pS45
hetero molecules

A: 14-3-3 protein sigma
P: p65pS45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5356
Polymers55,9434
Non-polymers5932
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4600 Å2
ΔGint-17 kcal/mol
Surface area22900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.598, 112.444, 62.555
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 p65pS45


Mass: 1412.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q04206*PLUS
#3: Chemical ChemComp-P7E / 4-(4-ethanoylpiperazin-1-yl)sulfonylbenzaldehyde


Mass: 296.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16N2O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
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: 2.6 Å3/Da / Density % sol: 52.63 %
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→56.22 Å / Num. obs: 57549 / % possible obs: 100 % / Redundancy: 1.9 % / Biso Wilson estimate: 10.05 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.046 / Rrim(I) all: 0.065 / Net I/σ(I): 11.1
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
1.4-1.421.90.157544827970.9220.1570.2234.3100
7.67-56.221.70.0466794080.9860.0460.06416.999.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.42
Highest resolutionLowest resolution
Rotation56.22 Å1.54 Å

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
MOLREPphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QHL

6qhl


Resolution: 1.4→34.465 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.75
RfactorNum. reflection% reflectionSelection details
Rfree0.1925 5580 5.04 %random
Rwork0.1712 ---
obs0.1723 57549 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 65.34 Å2 / Biso mean: 15.4074 Å2 / Biso min: 5.12 Å2
Refinement stepCycle: final / Resolution: 1.4→34.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1877 0 19 333 2229
Biso mean--11.56 25.89 -
Num. residues----243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092025
X-RAY DIFFRACTIONf_angle_d1.0632746
X-RAY DIFFRACTIONf_chiral_restr0.074298
X-RAY DIFFRACTIONf_plane_restr0.007363
X-RAY DIFFRACTIONf_dihedral_angle_d6.6371192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.4-1.41590.27861520.23193480
1.4159-1.43260.22991800.22323480
1.4326-1.450.20331690.19623562
1.45-1.46840.23041900.18593484
1.4684-1.48770.21232040.18153531
1.4877-1.50810.20061850.18553471
1.5081-1.52970.21181790.1773558
1.5297-1.55250.19991940.17453482
1.5525-1.57670.19262300.17633463
1.5767-1.60260.18381640.17713492
1.6026-1.63020.20632030.17323519
1.6302-1.65990.21231830.16743517
1.6599-1.69180.17962170.16283492
1.6918-1.72630.20261800.17053501
1.7263-1.76390.2172000.17813495
1.7639-1.80490.20881670.17773517
1.8049-1.850.19112110.17313497
1.85-1.90.20851690.17453515
1.9-1.95590.18642020.1773512
1.9559-2.01910.19731860.17133503
2.0191-2.09120.16571940.16233491
2.0912-2.17490.20552030.15953522
2.1749-2.27390.16851860.15063498
2.2739-2.39380.1762160.15943459
2.3938-2.54370.19881760.17343517
2.5437-2.740.17481660.17583546
2.74-3.01560.2321990.17923502
3.0156-3.45160.1641510.16723535
3.4516-4.34730.17741590.15493553
4.3473-34.4650.18151650.17643533

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