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- PDB-6y3v: 14-3-3 Sigma in complex with phosphorylated c-Jun peptide -

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Basic information

Entry
Database: PDB / ID: 6y3v
Title14-3-3 Sigma in complex with phosphorylated c-Jun peptide
Components
  • 14-3-3 protein sigma
  • c-Jun peptide
KeywordsPROTEIN BINDING / 14-3-3 / c-Jun / complex / protein / protein-protein interactions
Function / homology
Function and homology information


cAMP response element binding / transcription factor AP-1 complex / integrated stress response signaling / positive regulation of DNA-templated transcription initiation / release from viral latency / WNT5:FZD7-mediated leishmania damping / SMAD protein signal transduction / positive regulation by host of viral transcription / negative regulation of DNA binding / response to steroid hormone ...cAMP response element binding / transcription factor AP-1 complex / integrated stress response signaling / positive regulation of DNA-templated transcription initiation / release from viral latency / WNT5:FZD7-mediated leishmania damping / SMAD protein signal transduction / positive regulation by host of viral transcription / negative regulation of DNA binding / response to steroid hormone / nuclear chromosome / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Activation of the AP-1 family of transcription factors / regulation of cell-cell adhesion / R-SMAD binding / ubiquitin-like protein ligase binding / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / general transcription initiation factor binding / phosphoserine residue binding / negative regulation by host of viral transcription / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / 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 / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of cell adhesion / transforming growth factor beta receptor signaling pathway / GTPase activator activity / protein sequestering activity / negative regulation of innate immune response / response to endoplasmic reticulum stress / protein export from nucleus / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Regulation of PTEN gene transcription / positive regulation of protein export from nucleus / negative regulation of protein kinase activity / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / TP53 Regulates Transcription of DNA Repair Genes / FCERI mediated MAPK activation / euchromatin / MAPK6/MAPK4 signaling / Pre-NOTCH Transcription and Translation / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RNA polymerase II transcription regulator complex / intrinsic apoptotic signaling pathway in response to DNA damage / sequence-specific double-stranded DNA binding / Signaling by ALK fusions and activated point mutants / intracellular protein localization / regulation of protein localization / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / transcription regulator complex / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / regulation of cell cycle / cadherin binding / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular space / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Transcription factor Jun / Jun-like transcription factor / Jun-like transcription factor / bZIP transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / : / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain ...Transcription factor Jun / Jun-like transcription factor / Jun-like transcription factor / bZIP transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / : / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / 14-3-3 domain / Delta-Endotoxin; domain 1 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription factor Jun / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 Å
AuthorsBallone, A. / Lau, R.A. / Zweipfenning, F.P.A. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITN675179 Netherlands
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: A new soaking procedure for X-ray crystallographic structural determination of protein-peptide complexes.
Authors: Ballone, A. / Lau, R.A. / Zweipfenning, F.P.A. / Ottmann, C.
History
DepositionFeb 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / 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: c-Jun peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8426
Polymers29,7132
Non-polymers1294
Water8,323462
1
A: 14-3-3 protein sigma
P: c-Jun peptide
hetero molecules

A: 14-3-3 protein sigma
P: c-Jun peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,68412
Polymers59,4264
Non-polymers2588
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3160 Å2
ΔGint-54 kcal/mol
Surface area23450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.683, 112.054, 62.578
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-304-

CA

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Components

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 28210.518 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 c-Jun peptide


Mass: 1502.725 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P05412*PLUS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.74 Å3/Da / Density % sol: 55.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 28% (v/v) PEG400, 1.25% glycerol, 0.2M CaCl, 0.1M HEPES pH 7.5, 2mM BME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.499→66.531 Å / Num. obs: 46803 / % possible obs: 99 % / Redundancy: 11.9 % / Biso Wilson estimate: 11.52 Å2 / CC1/2: 0.483 / Net I/σ(I): 3.7
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 2252 / CC1/2: 0.289

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
REFMAC5.5refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LW1

3lw1


Resolution: 1.499→66.531 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5
RfactorNum. reflection% reflection
Rfree0.221 2319 4.95 %
Rwork0.1925 --
obs0.194 46803 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.499→66.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 14 462 2308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051882
X-RAY DIFFRACTIONf_angle_d0.7282537
X-RAY DIFFRACTIONf_dihedral_angle_d5.7511153
X-RAY DIFFRACTIONf_chiral_restr0.059280
X-RAY DIFFRACTIONf_plane_restr0.004332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4991-1.52970.30671340.26652578X-RAY DIFFRACTION98
1.5297-1.5630.3161000.25282600X-RAY DIFFRACTION99
1.563-1.59930.28051380.25072555X-RAY DIFFRACTION100
1.5993-1.63930.26911310.23452583X-RAY DIFFRACTION100
1.6393-1.68360.25941310.22672596X-RAY DIFFRACTION100
1.6836-1.73320.26711450.22532597X-RAY DIFFRACTION100
1.7332-1.78910.26251380.22582605X-RAY DIFFRACTION100
1.7891-1.85310.27171670.222537X-RAY DIFFRACTION100
1.8531-1.92730.22171300.20642610X-RAY DIFFRACTION100
1.9273-2.0150.25421240.19362622X-RAY DIFFRACTION100
2.015-2.12130.22481440.17942614X-RAY DIFFRACTION100
2.1213-2.25420.17931370.17552607X-RAY DIFFRACTION100
2.2542-2.42820.19851220.17482647X-RAY DIFFRACTION100
2.4282-2.67260.22881370.17922647X-RAY DIFFRACTION100
2.6726-3.05930.2081300.18562640X-RAY DIFFRACTION100
3.0593-3.85440.19241560.16682669X-RAY DIFFRACTION100
3.8544-66.530.19191550.17742777X-RAY DIFFRACTION100

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