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- PDB-6yos: Binary complex of 14-3-3 zeta with Glucocorticoid Receptor (GR) p... -

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Basic information

Entry
Database: PDB / ID: 6yos
TitleBinary complex of 14-3-3 zeta with Glucocorticoid Receptor (GR) pT524 pS617 peptide
Components
  • 14-3-3 protein zeta/delta
  • Glucocorticoid receptor,Glucocorticoid receptor
KeywordsPROTEIN BINDING / 14-3-3 protein zeta/delta / glucocorticoid Receptor / protein-peptide complex / protein-protein interaction
Function / homology
Function and homology information


Regulation of NPAS4 gene transcription / Golgi reassembly / synaptic target recognition / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / neuroinflammatory response / glucocorticoid metabolic process / NOTCH4 Activation and Transmission of Signal to the Nucleus ...Regulation of NPAS4 gene transcription / Golgi reassembly / synaptic target recognition / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / neuroinflammatory response / glucocorticoid metabolic process / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / tube formation / respiratory system process / mammary gland duct morphogenesis / microglia differentiation / regulation of synapse maturation / maternal behavior / Rap1 signalling / astrocyte differentiation / negative regulation of protein localization to nucleus / cellular response to glucocorticoid stimulus / motor behavior / KSRP (KHSRP) binds and destabilizes mRNA / adrenal gland development / cellular response to steroid hormone stimulus / GP1b-IX-V activation signalling / regulation of gluconeogenesis / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / Activation of BAD and translocation to mitochondria / protein targeting / estrogen response element binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / nuclear receptor-mediated steroid hormone signaling pathway / cellular response to glucose starvation / core promoter sequence-specific DNA binding / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / cellular response to transforming growth factor beta stimulus / negative regulation of TORC1 signaling / negative regulation of innate immune response / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein sequestering activity / steroid binding / TBP-class protein binding / ERK1 and ERK2 cascade / regulation of ERK1 and ERK2 cascade / hippocampal mossy fiber to CA3 synapse / cellular response to dexamethasone stimulus / synaptic transmission, glutamatergic / chromosome segregation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / RNA polymerase II transcription regulatory region sequence-specific DNA binding / lung development / Negative regulation of NOTCH4 signaling / SUMOylation of intracellular receptors / Hsp90 protein binding / regulation of protein stability / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / spindle / positive regulation of neuron apoptotic process / nuclear receptor activity / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / protein localization / Circadian Clock / melanosome / chromatin organization / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / DNA-binding transcription factor binding / vesicle / blood microparticle / transmembrane transporter binding / Potential therapeutics for SARS / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / mitochondrial matrix / cadherin binding / protein phosphorylation / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / cell division / focal adhesion / negative regulation of DNA-templated transcription / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / synapse / regulation of DNA-templated transcription / chromatin
Similarity search - Function
Glucocorticoid receptor / Glucocorticoid receptor / 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 ...Glucocorticoid receptor / Glucocorticoid receptor / 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 / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type
Similarity search - Domain/homology
Glucocorticoid receptor / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsMunier, C.C. / Edman, K. / Perry, M.W.D. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European Commission675179 Netherlands
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Glucocorticoid receptor Thr524 phosphorylation by MINK1 induces interactions with 14-3-3 protein regulators.
Authors: Munier, C.C. / De Maria, L. / Edman, K. / Gunnarsson, A. / Longo, M. / MacKintosh, C. / Patel, S. / Snijder, A. / Wissler, L. / Brunsveld, L. / Ottmann, C. / Perry, M.W.D.
History
DepositionApr 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
C: Glucocorticoid receptor,Glucocorticoid receptor


Theoretical massNumber of molelcules
Total (without water)56,7943
Polymers56,7943
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-27 kcal/mol
Surface area23310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.206, 60.206, 284.213
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein 14-3-3 protein zeta/delta / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 26720.217 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Plasmid: pProEx Htb / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: P63104
#2: Protein/peptide Glucocorticoid receptor,Glucocorticoid receptor / GR / Nuclear receptor subfamily 3 group C member 1


Mass: 3353.616 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04150
Has ligand of interestN

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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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 293.15 K / Method: evaporation / pH: 6.8
Details: 0.35 M MgCl2, 24.4% PEG 3350, 0. 1 M Bis Tris pH 5.5 supplemented with 10% of an additive buffer containing 0.06 M CHAPS, 0.06 M HEPES, 0.06 M Tris, 0.25% w/v Hexamminecobalt(III) chloride ...Details: 0.35 M MgCl2, 24.4% PEG 3350, 0. 1 M Bis Tris pH 5.5 supplemented with 10% of an additive buffer containing 0.06 M CHAPS, 0.06 M HEPES, 0.06 M Tris, 0.25% w/v Hexamminecobalt(III) chloride and 0.02 M HEPES sodium pH 6.8.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 2.75→58.9 Å / Num. obs: 14321 / % possible obs: 98.3 % / Redundancy: 9.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.036 / Rrim(I) all: 0.116 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) all% possible allRrim(I) all
2.75-2.96.91.60619090.6260.60794
8.7-58.98.70.0385700.9990.01399.70.041

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
Aimless0.5.21data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O02

2o02


Resolution: 2.75→58.9 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.883 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.369
RfactorNum. reflection% reflectionSelection details
Rfree0.261 675 4.74 %RANDOM
Rwork0.239 ---
obs0.24 14250 98.1 %-
Displacement parametersBiso max: 176.59 Å2 / Biso min: 52.07 Å2
Baniso -1Baniso -2Baniso -3
1-14.6384 Å20 Å20 Å2
2--14.6384 Å20 Å2
3----29.2768 Å2
Refine analyzeLuzzati coordinate error obs: 0.52 Å
Refinement stepCycle: final / Resolution: 2.75→58.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3698 0 0 0 3698
Num. residues----461
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1380SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes638HARMONIC5
X-RAY DIFFRACTIONt_it3745HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion486SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4441SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3745HARMONIC20.018
X-RAY DIFFRACTIONt_angle_deg5038HARMONIC21.46
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion22.07
LS refinement shellResolution: 2.75→2.78 Å / Rfactor Rfree error: 0 / Total num. of bins used: 33
RfactorNum. reflection% reflection
Rfree0.2866 19 4.4 %
Rwork0.2868 413 -
all0.2868 432 -
obs--95.08 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.4826-0.8918-0.95853.36990.07852.36920.01580.06580.2285-0.15560.036-0.3623-0.1650.0174-0.0519-0.5615-0.09460.0882-0.5752-0.0412-0.5876-4.6552-19.7266-22.9865
22.8042-1.60171.00053.7879-1.42382.10570.3911.30590.9324-1.2051-0.7656-0.0299-0.05870.24230.37460.09220.22240.07560.34630.21730.31166.782-16.2614-54.2522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|230 }A1 - 230
2X-RAY DIFFRACTION2{ B|1 - B|229 }B1 - 229

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