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

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Basic information

Entry
Database: PDB / ID: 6ypl
Title14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521-037
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 / Purinergic signaling in leishmaniasis infection / RNA polymerase II core promoter sequence-specific DNA binding / 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 / NF-kB is activated and signals survival / response to interleukin-1 / protein sequestering activity / protein export from nucleus / response to progesterone / negative regulation of innate immune response / negative regulation of miRNA transcription / 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
(2-methylsulfonylphenyl)methanol / 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 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 1.4Nov 20, 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: p65pS45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1934
Polymers27,9712
Non-polymers2222
Water5,062281
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)56,3868
Polymers55,9434
Non-polymers4434
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4960 Å2
ΔGint-44 kcal/mol
Surface area23000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.667, 112.708, 62.765
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-P6H / (2-methylsulfonylphenyl)methanol


Mass: 186.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.61 Å3/Da / Density % sol: 52.93 %
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: 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→66.66 Å / Num. obs: 27597 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 12.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.031 / Rrim(I) all: 0.077 / Net I/σ(I): 17.1
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
1.8-1.844.70.289720215420.9470.1460.3253.295.9
8.99-66.665.10.018135126510.0090.0243.199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.372
Highest resolutionLowest resolution
Rotation66.71 Å1.9 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→66.659 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 22.45
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 2674 5.1 %random
Rwork0.1959 ---
obs0.1976 27597 99.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.89 Å2 / Biso mean: 16.9619 Å2 / Biso min: 3.36 Å2
Refinement stepCycle: final / Resolution: 1.8→66.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 12 281 2186
Biso mean--33.56 24.9 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031980
X-RAY DIFFRACTIONf_angle_d0.6052674
X-RAY DIFFRACTIONf_chiral_restr0.034291
X-RAY DIFFRACTIONf_plane_restr0.003352
X-RAY DIFFRACTIONf_dihedral_angle_d5.2861649
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.83070.3171330.2804238991
1.8307-1.8660.31631130.25782628100
1.866-1.9040.29261500.2462635100
1.904-1.94550.24761590.2022622100
1.9455-1.99070.26811330.21252632100
1.9907-2.04050.26031160.21322658100
2.0405-2.09570.23921490.19732599100
2.0957-2.15730.25491610.20562618100
2.1573-2.2270.22461200.19822663100
2.227-2.30660.20121180.18982669100
2.3066-2.39890.24241250.19752624100
2.3989-2.50810.26851540.21032644100
2.5081-2.64040.27491440.19212613100
2.6404-2.80580.22061600.20022611100
2.8058-3.02240.20741610.20572619100
3.0224-3.32660.1821400.18622640100
3.3266-3.80790.22391660.16782590100
3.8079-4.79730.18881550.16422626100
4.7973-66.6590.20671170.18692660100

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