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- PDB-6yo8: Binary complex of 14-3-3 zeta with Glucocorticoid Receptor (GR) p... -

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Basic information

Entry
Database: PDB / ID: 6yo8
TitleBinary complex of 14-3-3 zeta with Glucocorticoid Receptor (GR) pT524 peptide
Components
  • 14-3-3 protein zeta/delta
  • 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 / regulation of synapse maturation / PTK6 Expression / NOTCH4 Activation and Transmission of Signal to the Nucleus / respiratory system process ...Regulation of NPAS4 gene transcription / Golgi reassembly / synaptic target recognition / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / regulation of synapse maturation / PTK6 Expression / NOTCH4 Activation and Transmission of Signal to the Nucleus / respiratory system process / neuroinflammatory response / glucocorticoid metabolic process / establishment of Golgi localization / microglia differentiation / mammary gland duct morphogenesis / maternal behavior / tube formation / Rap1 signalling / astrocyte differentiation / cellular response to glucocorticoid stimulus / negative regulation of protein localization to nucleus / motor behavior / KSRP (KHSRP) binds and destabilizes mRNA / regulation of gluconeogenesis / adrenal gland development / cellular response to steroid hormone stimulus / GP1b-IX-V activation signalling / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / 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 / cellular response to glucose starvation / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / intracellular steroid hormone receptor signaling pathway / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / core promoter sequence-specific DNA binding / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / cellular response to transforming growth factor beta stimulus / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ERK1 and ERK2 cascade / TBP-class protein binding / negative regulation of innate immune response / steroid binding / protein sequestering activity / hippocampal mossy fiber to CA3 synapse / cellular response to dexamethasone stimulus / regulation of ERK1 and ERK2 cascade / synaptic transmission, glutamatergic / chromosome segregation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / lung development / SUMOylation of intracellular receptors / regulation of protein stability / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / spindle / Regulation of RUNX2 expression and activity / nuclear receptor activity / positive regulation of neuron apoptotic process / sequence-specific double-stranded DNA binding / melanosome / Circadian Clock / chromatin organization / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / angiogenesis / vesicle / transmembrane transporter binding / Potential therapeutics for SARS / blood microparticle / DNA-binding transcription factor activity, RNA polymerase II-specific / mitochondrial matrix / nuclear speck / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / cell division / protein phosphorylation / focal adhesion / negative regulation of DNA-templated transcription / centrosome / glutamatergic synapse / apoptotic process / synapse / ubiquitin protein ligase binding / chromatin / regulation of DNA-templated transcription
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: 2.09 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 14, 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: 14-3-3 protein zeta/delta
D: 14-3-3 protein zeta/delta
E: Glucocorticoid receptor
F: Glucocorticoid receptor
G: Glucocorticoid receptor
H: Glucocorticoid receptor


Theoretical massNumber of molelcules
Total (without water)112,7198
Polymers112,7198
Non-polymers00
Water4,324240
1
A: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
E: Glucocorticoid receptor
F: Glucocorticoid receptor


Theoretical massNumber of molelcules
Total (without water)56,3604
Polymers56,3604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-35 kcal/mol
Surface area23730 Å2
MethodPISA
2
C: 14-3-3 protein zeta/delta
D: 14-3-3 protein zeta/delta
G: Glucocorticoid receptor
H: Glucocorticoid receptor


Theoretical massNumber of molelcules
Total (without water)56,3604
Polymers56,3604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-37 kcal/mol
Surface area23700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.651, 99.880, 84.812
Angle α, β, γ (deg.)90.000, 93.730, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

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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.: 4
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 / / GR / Nuclear receptor subfamily 3 group C member 1


Mass: 1459.642 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04150
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.01 Å3/Da / Density % sol: 59.1 %
Crystal growTemperature: 277.15 K / Method: evaporation / pH: 8.3
Details: 1.29 M MgCl2, 22.5% PEG 3350, 0.1 M Tris pH 8.3, supplemented with 10% of an additive buffer containing 40% v/v of 2,5-Hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.086→84.474 Å / Num. obs: 77152 / % possible obs: 98.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 60.34 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.039 / Rrim(I) all: 0.073 / Net I/σ(I): 9
Reflection shellResolution: 2.086→2.122 Å / Redundancy: 3.4 % / Num. unique obs: 3821 / CC1/2: 0.296 / % possible all: 97.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.6.2data scaling
PHASERphasing
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O02

2o02


Resolution: 2.09→60.85 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.193 / SU Rfree Blow DPI: 0.158 / SU Rfree Cruickshank DPI: 0.161
RfactorNum. reflection% reflectionSelection details
Rfree0.238 3841 5.01 %RANDOM
Rwork0.224 ---
obs0.225 76616 97.5 %-
Displacement parametersBiso max: 174.1 Å2 / Biso min: 39.22 Å2
Baniso -1Baniso -2Baniso -3
1--1.2573 Å20 Å26.0367 Å2
2--9.3356 Å20 Å2
3----8.0784 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: final / Resolution: 2.09→60.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7685 0 0 240 7925
Biso mean---67.97 -
Num. residues----961
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2860SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1333HARMONIC5
X-RAY DIFFRACTIONt_it7801HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1024SEMIHARMONIC5
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_contact9310SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7801HARMONIC20.014
X-RAY DIFFRACTIONt_angle_deg10522HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion20.75
LS refinement shellResolution: 2.09→2.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2308 83 5.41 %
Rwork0.2291 1450 -
all0.2292 1533 -
obs--81.22 %
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)
11.73740.9704-0.11664.20820.86731.696-0.14840.16590.2705-0.60860.00990.2555-0.07890.05230.1385-0.69020.0124-0.0581-0.68740.056-0.5934-23.721942.621931.1618
21.8129-1.1950.01873.78370.14981.26330.0294-0.2459-0.12060.23980.04940.37520.19510.0079-0.0788-0.6744-0.0350.0416-0.68990.0263-0.6555-26.91265.505642.0244
31.502-0.14290.60592.5709-1.31054.51550.0350.07440.0718-0.0855-0.2337-0.1752-0.04850.74830.1987-0.7851-0.0672-0.0015-0.66710.0431-0.8203-51.321627.33-13.5562
41.98150.097-0.81532.32120.87454.9878-0.1722-0.254-0.03970.06840.07270.11690.12950.3930.0995-0.77710.0529-0.0855-0.68940.0402-0.7941-60.373419.002723.1938
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 230
2X-RAY DIFFRACTION2{ B|* }B1 - 230
3X-RAY DIFFRACTION3{ C|* }C1 - 230
4X-RAY DIFFRACTION4{ D|* }D1 - 230

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