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

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Basic information

Entry
Database: PDB / ID: 7nqp
Title14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound LvD1009
Components
  • 14-3-3 protein sigma
  • Transcription factor p65
KeywordsPEPTIDE BINDING PROTEIN / benzaldehyde / 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 / 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
2-bromanyl-4-(2-phenylimidazol-1-yl)benzaldehyde / 14-3-3 protein sigma / Transcription factor p65
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.24 Å
AuthorsWolter, M. / Dijck, L.v. / Cossar, P.J. / Ottmann, C.
Funding support2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission675179
H2020 Marie Curie Actions of the European Commission754462
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Reversible Covalent Imine-Tethering for Selective Stabilization of 14-3-3 Hub Protein Interactions.
Authors: Cossar, P.J. / Wolter, M. / van Dijck, L. / Valenti, D. / Levy, L.M. / Ottmann, C. / Brunsveld, L.
History
DepositionMar 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 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 6, 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

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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)29,9904
Polymers29,6392
Non-polymers3512
Water4,972276
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)59,9818
Polymers59,2784
Non-polymers7034
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4770 Å2
ΔGint-30 kcal/mol
Surface area21840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.408, 112.028, 62.602
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: 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 / Source method: obtained synthetically / Details: alternative sequencing (E49R) with ID CAA80524 / Source: (synth.) Homo sapiens (human) / References: UniProt: Q04206
#3: Chemical ChemComp-TJ8 / 2-bromanyl-4-(2-phenylimidazol-1-yl)benzaldehyde / LvD1009


Mass: 327.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H11BrN2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
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: May 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.24→66.38 Å / Num. obs: 81921 / % possible obs: 99.8 % / Redundancy: 12 % / Biso Wilson estimate: 14.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.03 / Rrim(I) all: 0.106 / Net I/σ(I): 11.1 / Num. measured all: 985833 / Scaling rejects: 1632
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
1.24-1.278.11.7344779458980.6360.631.851197.8
5.55-66.3812.30.0771258410220.9970.0220.0830.999.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
MOLREPphasing
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QHL

6qhl


Resolution: 1.24→66.38 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2169 4082 4.99 %
Rwork0.1954 77775 -
obs0.1964 81857 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.17 Å2 / Biso mean: 20.4706 Å2 / Biso min: 9.17 Å2
Refinement stepCycle: final / Resolution: 1.24→66.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 20 276 2129
Biso mean--33.3 32.79 -
Num. residues----236
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.24-1.250.42111330.40592552268596
1.25-1.270.38771340.36382627276198
1.27-1.290.2751500.29032634278499
1.29-1.30.26461400.26142657279799
1.3-1.320.26451450.259826192764100
1.32-1.340.31611350.267226912826100
1.34-1.360.27881620.255826432805100
1.36-1.380.26431510.255926302781100
1.38-1.40.27651450.254926572802100
1.4-1.430.22241370.242926622799100
1.43-1.450.26261490.229626802829100
1.45-1.480.24781280.206526812809100
1.48-1.510.20151270.201826692796100
1.51-1.540.23341550.197126702825100
1.54-1.580.24031430.197926702813100
1.58-1.620.21261350.187126872822100
1.62-1.660.18581160.189926882804100
1.66-1.710.20661260.191726942820100
1.71-1.770.22531540.197726832837100
1.77-1.830.20651470.202926912838100
1.83-1.90.21871670.202726352802100
1.9-1.990.22021400.188327162856100
1.99-2.10.19181690.177926662835100
2.1-2.230.19811290.178227222851100
2.23-2.40.18841310.171627242855100
2.4-2.640.20591380.18327012839100
2.64-3.020.21031230.192627782901100
3.02-3.810.22631130.178827832896100
3.81-66.380.19711600.184128653025100

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