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- PDB-6yp3: 14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound... -

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Basic information

Entry
Database: PDB / ID: 6yp3
Title14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-028
Components
  • 14-3-3 protein sigma
  • p65pS45
KeywordsPEPTIDE BINDING PROTEIN / covalent fragment / p65 / 1433
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
1-(4-methylphenyl)-1,2,4-triazole / 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
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 15, 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 23, 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)28,1664
Polymers27,9712
Non-polymers1952
Water5,837324
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)56,3328
Polymers55,9434
Non-polymers3894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4900 Å2
ΔGint-51 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.498, 112.220, 62.550
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-P5Q / 1-(4-methylphenyl)-1,2,4-triazole


Mass: 159.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9N3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.59 Å3/Da / Density % sol: 52.47 %
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: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.8→41.77 Å / Num. obs: 27260 / % possible obs: 99.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 11.72 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.036 / Rrim(I) all: 0.09 / Net I/σ(I): 17.9
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
1.8-1.844.10.35613415140.8860.1870.3992.893.8
8.99-41.7750.018129426110.0090.027399

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.371
Highest resolutionLowest resolution
Rotation41.27 Å1.89 Å

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
MOLREPphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QHL

6qhl


Resolution: 1.8→41.768 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 21.17
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 2620 5.08 %Random
Rwork0.1808 ---
obs0.1826 27260 98.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.89 Å2 / Biso mean: 15.9808 Å2 / Biso min: 2.44 Å2
Refinement stepCycle: final / Resolution: 1.8→41.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 13 324 2242
Biso mean--39.03 24.51 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041995
X-RAY DIFFRACTIONf_angle_d0.6212692
X-RAY DIFFRACTIONf_chiral_restr0.037291
X-RAY DIFFRACTIONf_plane_restr0.003357
X-RAY DIFFRACTIONf_dihedral_angle_d5.7841664
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.83120.30881050.2498229187
1.8312-1.86640.25581200.2348250297
1.8664-1.90450.27211470.2302255599
1.9045-1.94590.26361520.2129258399
1.9459-1.99110.22151330.2028261099
1.9911-2.04090.25811150.1923259899
2.0409-2.09610.19511520.1733256599
2.0961-2.15780.22881520.17622593100
2.1578-2.22740.19361220.17272649100
2.2274-2.3070.1981140.17092593100
2.307-2.39940.24191240.17542650100
2.3994-2.50860.25451470.18732583100
2.5086-2.64080.26681420.17952578100
2.6408-2.80630.20461720.18982596100
2.8063-3.02290.21461520.19232591100
3.0229-3.3270.20511370.16882622100
3.327-3.80810.21171660.15732553100
3.8081-4.79670.15921550.14922589100
4.7967-41.7680.17931130.18362635100

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