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- PDB-7o5x: 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound... -

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Basic information

Entry
Database: PDB / ID: 7o5x
Title14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-173
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 / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 ...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 / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / Regulated proteolysis of p75NTR / 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 / Interleukin-1 processing / 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 / positive regulation of miRNA metabolic process / vascular endothelial growth factor signaling pathway / non-canonical NF-kappaB signal transduction / 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 / response to cobalamin / keratinization / positive regulation of T cell receptor signaling pathway / phosphate ion binding / regulation of cell-cell adhesion / cellular response to lipoteichoic acid / response to muramyl dipeptide / TRAF6 mediated NF-kB activation / The NLRP3 inflammasome / Regulation of localization of FOXO transcription factors / general transcription initiation factor binding / keratinocyte proliferation / Transcriptional Regulation by VENTX / neuropeptide signaling pathway / cellular response to interleukin-1 / phosphoserine residue binding / NF-kappaB binding / hair follicle development / positive regulation of vascular endothelial growth factor production / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / 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 / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Purinergic signaling in leishmaniasis infection / 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 / response to cAMP / response to muscle stretch / protein kinase A signaling / protein sequestering activity / positive regulation of interleukin-12 production / protein export from nucleus / negative regulation of innate immune response / CD209 (DC-SIGN) signaling / positive regulation of cell adhesion / NF-kB is activated and signals survival / response to interleukin-1 / negative regulation of angiogenesis / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / negative regulation of miRNA transcription / positive regulation of protein export from nucleus / liver development / stem cell proliferation / response to cytokine / positive regulation of interleukin-1 beta production / response to ischemia / positive regulation of interleukin-8 production / response to progesterone / Translocation of SLC2A4 (GLUT4) to the plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / TP53 Regulates Metabolic Genes
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 / 4-(4-methoxypiperidin-1-yl)carbonylbenzaldehyde / 14-3-3 protein sigma / Transcription factor p65
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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
DepositionApr 9, 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 1.3Nov 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

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)28,4367
Polymers27,9712
Non-polymers4645
Water5,008278
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)56,87114
Polymers55,9434
Non-polymers92910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5280 Å2
ΔGint-66 kcal/mol
Surface area22280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.478, 112.233, 62.605
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-

CA

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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, 283 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-V3W / 4-(4-methoxypiperidin-1-yl)carbonylbenzaldehyde


Mass: 247.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#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.: 278 / 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: 2.59 Å3/Da / Density % sol: 52.51 % / 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: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.8→34.07 Å / Num. obs: 26174 / % possible obs: 96 % / Redundancy: 5.7 % / Biso Wilson estimate: 13.43 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.036 / Rrim(I) all: 0.09 / Net I/σ(I): 14.2
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
1.8-1.851.50.24174111740.8830.2120.3211.759.6
8.05-34.0550.02417613510.9990.0120.02737.998.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
Aimless0.7.2data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QHL

6qhl


Resolution: 1.8→34.07 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 21.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2189 1323 5.06 %
Rwork0.1847 24834 -
obs0.1864 26157 95.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.37 Å2 / Biso mean: 16.5734 Å2 / Biso min: 3.23 Å2
Refinement stepCycle: final / Resolution: 1.8→34.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1831 0 27 278 2136
Biso mean--33.78 25.95 -
Num. residues----236
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.870.2891020.23781964206669
1.87-1.960.23971530.21272671282495
1.96-2.060.23131540.18922813296799
2.06-2.190.21481380.177528522990100
2.19-2.360.21911510.180828533004100
2.36-2.60.20411570.193328753032100
2.6-2.970.25431600.194828733033100
2.97-3.740.2191480.174529153063100
3.74-34.070.18861600.170530183178100

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