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

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Basic information

Entry
Database: PDB / ID: 7nvi
Title14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-186
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 / Regulated proteolysis of p75NTR / ankyrin repeat binding ...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 / Regulated proteolysis of p75NTR / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / Interleukin-1 processing / 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 / 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 / non-canonical NF-kappaB signal transduction / positive regulation of miRNA metabolic process / 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 / positive regulation of T cell receptor signaling pathway / response to cobalamin / keratinization / phosphate ion binding / regulation of cell-cell adhesion / cellular response to lipoteichoic acid / TRAF6 mediated NF-kB activation / response to muramyl dipeptide / The NLRP3 inflammasome / Regulation of localization of FOXO transcription factors / general transcription initiation factor binding / keratinocyte proliferation / Transcriptional Regulation by VENTX / cellular response to interleukin-1 / phosphoserine residue binding / NF-kappaB binding / negative regulation of keratinocyte proliferation / positive regulation of vascular endothelial growth factor production / hair follicle development / neuropeptide signaling pathway / Activation of BAD and translocation to mitochondria / 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 / Purinergic signaling in leishmaniasis infection / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / 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 / negative regulation of innate immune response / response to cAMP / protein sequestering activity / protein kinase A signaling / response to muscle stretch / positive regulation of interleukin-12 production / protein export from nucleus / CD209 (DC-SIGN) signaling / NF-kB is activated and signals survival / positive regulation of cell adhesion / response to interleukin-1 / negative regulation of angiogenesis / release of cytochrome c from mitochondria / liver development / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of miRNA transcription / response to cytokine / positive regulation of protein export from nucleus / positive regulation of interleukin-1 beta production / stem cell proliferation / positive regulation of interleukin-8 production / response to ischemia / response to progesterone / Translocation of SLC2A4 (GLUT4) to the plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / animal organ morphogenesis
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
DI(HYDROXYETHYL)ETHER / Chem-USW / 14-3-3 protein sigma / Transcription factor p65
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 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
DepositionMar 15, 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 1.3Oct 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: Transcription factor p65
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5107
Polymers27,9712
Non-polymers5395
Water4,774265
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)57,02114
Polymers55,9434
Non-polymers1,07810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6110 Å2
ΔGint-49 kcal/mol
Surface area21620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.233, 112.401, 62.425
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-304-

MG

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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: 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 / 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: the sequence follows an alternative sequencing (ID: CAA80524)
Source: (synth.) Homo sapiens (human) / References: UniProt: Q04206

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Non-polymers , 5 types, 270 molecules

#3: Chemical ChemComp-USW / 4-[(7-chloranyl-2,3-dihydro-1,4-benzoxazin-4-yl)sulfonyl]benzaldehyde


Mass: 337.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12ClNO4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.58 Å3/Da / Density % sol: 52.3 % / 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: I03 / Wavelength: 0.976284 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976284 Å / Relative weight: 1
ReflectionResolution: 1.2→66.37 Å / Num. obs: 89941 / % possible obs: 99.6 % / Redundancy: 12.8 % / Biso Wilson estimate: 13.09 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.012 / Rrim(I) all: 0.042 / Net I/σ(I): 28.2
Reflection shell

Diffraction-ID: 1 / % possible all: 98.8

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.2-1.2212.90.4765590943440.9050.1360.4953.9
6.57-66.3711.40.0471366260.9550.0140.04388.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

6qhl


Resolution: 1.2→45.47 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.86 / Stereochemistry target values: ML / Details: MOLECULAR REPLACEMENT
RfactorNum. reflection% reflection
Rfree0.1951 4545 5.07 %
Rwork0.1819 165110 -
obs0.1826 89858 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.73 Å2 / Biso mean: 18.1879 Å2 / Biso min: 9.32 Å2
Refinement stepCycle: final / Resolution: 1.2→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1843 0 41 265 2149
Biso mean--27.28 26.91 -
Num. residues----237
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.210.26083040.245391569598
1.21-1.230.25883180.23225398571699
1.23-1.240.27462530.23025537579099
1.24-1.260.25292820.21915379566199
1.26-1.280.22493540.22175472582699
1.28-1.290.23333390.21055416575599
1.29-1.310.21143150.20985458577399
1.31-1.330.24183350.21115412574799
1.33-1.350.20232880.20745504579299
1.35-1.370.21593250.20685495582099
1.37-1.40.23093080.20935526583499
1.4-1.420.21732890.20475459574899
1.42-1.450.2033180.198954915809100
1.45-1.480.20463120.187654955807100
1.48-1.510.18832950.17955565851100
1.51-1.550.19433090.174954545763100
1.55-1.590.17472650.180156005865100
1.59-1.630.17272790.173754655744100
1.63-1.680.20112950.168655625857100
1.68-1.730.16642780.176655545832100
1.73-1.790.21182770.183455335810100
1.79-1.860.19572830.189755385821100
1.86-1.950.17792690.182355805849100
1.95-2.050.20322530.17855155768100
2.05-2.180.1892750.167455955870100
2.18-2.350.1592520.168855515803100
2.35-2.590.19683010.178755515852100
2.59-2.960.21662810.189855195800100
2.96-3.730.19372760.180555695845100
3.73-45.470.1722890.165955355824100

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