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

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Basic information

Entry
Database: PDB / ID: 6ymo
TitleBinary complex of 14-3-3 zeta with Glucocorticoid Receptor (GR) pS617 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 / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / synaptic target recognition / Golgi reassembly / steroid hormone binding / glucocorticoid metabolic process / response to cortisol / PTK6 Expression / neuroinflammatory response ...Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / synaptic target recognition / Golgi reassembly / steroid hormone binding / glucocorticoid metabolic process / response to cortisol / PTK6 Expression / neuroinflammatory response / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / mammary gland duct morphogenesis / microglia differentiation / respiratory system process / tube formation / regulation of synapse maturation / maternal behavior / astrocyte differentiation / Rap1 signalling / negative regulation of protein localization to nucleus / adrenal gland development / KSRP (KHSRP) binds and destabilizes mRNA / regulation of gluconeogenesis / cellular response to glucocorticoid stimulus / GP1b-IX-V activation signalling / cellular response to steroid hormone stimulus / motor behavior / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / estrogen response element binding / Activation of BAD and translocation to mitochondria / nuclear receptor-mediated steroid hormone signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cellular response to transforming growth factor beta stimulus / protein targeting / regulation of ERK1 and ERK2 cascade / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / core promoter sequence-specific DNA binding / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / steroid binding / ERK1 and ERK2 cascade / cellular response to dexamethasone stimulus / Transcriptional and post-translational regulation of MITF-M expression and activity / protein sequestering activity / Deactivation of the beta-catenin transactivating complex / negative regulation of innate immune response / TBP-class protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / hippocampal mossy fiber to CA3 synapse / Negative regulation of NOTCH4 signaling / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / synaptic transmission, glutamatergic / chromosome segregation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / lung development / Hsp90 protein binding / promoter-specific chromatin binding / regulation of protein stability / Nuclear Receptor transcription pathway / positive regulation of miRNA transcription / response to wounding / DNA-binding transcription repressor activity, RNA polymerase II-specific / spindle / Regulation of RUNX2 expression and activity / nuclear receptor activity / : / sequence-specific double-stranded DNA binding / melanosome / intracellular protein localization / positive regulation of neuron apoptotic process / chromatin organization / DNA-binding transcription activator activity, RNA polymerase II-specific / blood microparticle / vesicle / angiogenesis / protein phosphatase binding / DNA-binding transcription factor binding / Potential therapeutics for SARS / gene expression / transmembrane transporter binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / protein phosphorylation / cadherin binding / mitochondrial matrix / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / cell division / focal adhesion / negative regulation of DNA-templated transcription / apoptotic process
Similarity search - Function
Glucocorticoid receptor / Glucocorticoid receptor / 14-3-3 domain / Delta-Endotoxin; domain 1 / 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 ...Glucocorticoid receptor / Glucocorticoid receptor / 14-3-3 domain / Delta-Endotoxin; domain 1 / 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 / Double treble clef zinc finger, C4 type / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
2-HYDROXYBENZOIC ACID / Glucocorticoid receptor / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.02 Å
AuthorsMunier, C.C. / Edman, K. / Perry, M.W.D. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the 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 9, 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 1.2May 5, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.3Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Jan 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 1.5Oct 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 zeta/delta
B: 14-3-3 protein zeta/delta
C: Glucocorticoid receptor
D: Glucocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9286
Polymers56,6944
Non-polymers2342
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-26 kcal/mol
Surface area23310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.285, 104.351, 112.429
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 / GR / Nuclear receptor subfamily 3 group C member 1


Mass: 1626.731 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04150
#3: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 3.74 Å3/Da / Density % sol: 67.11 %
Crystal growTemperature: 277.15 K / Method: evaporation / pH: 6.8
Details: 2.04 M ammonium sulfate, 0.2 M sodium citrate supplemented with 10% of an additive buffer containing 0.33% w/v 3-aminobenzoic acid, 0.33% w/v 3-aminosalicylic acid, 0.33% w/v salicylic acid ...Details: 2.04 M ammonium sulfate, 0.2 M sodium citrate supplemented with 10% of an additive buffer containing 0.33% w/v 3-aminobenzoic acid, 0.33% w/v 3-aminosalicylic acid, 0.33% w/v salicylic acid 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: Jan 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 2.02→47.33 Å / Num. obs: 56557 / % possible obs: 99.6 % / Redundancy: 6.483 % / Biso Wilson estimate: 53.52 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.089 / Χ2: 1.025 / Net I/σ(I): 12.07 / Num. measured all: 366684 / Scaling rejects: 73
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2% possible allRmerge(I) obsRrim(I) all
2.02-2.076.3440.5339570.22695.8
2.07-2.136.4570.7840670.3199.9
2.13-2.196.4021.1539120.4551001.707
2.19-2.256.1481.5538220.55699.81.273
2.25-2.336.3672.0936860.76299.90.98
2.33-2.416.6282.8435880.86899.90.7120.773
2.41-2.56.843.6134760.9191000.5620.608
2.5-2.66.7234.7133450.9461000.4280.464
2.6-2.726.3666.0731870.9641000.3170.346
2.72-2.856.6588.430740.98799.90.2180.237
2.85-3.016.70511.1529500.9921000.1620.176
3.01-3.196.8115.7227830.9961000.1110.12
3.19-3.416.57126160.9971000.0790.086
3.41-3.686.41524280.99899.90.0560.061
3.68-4.036.43722800.9991000.0430.047
4.03-4.516.68820550.9991000.0360.039
4.51-5.216.25718180.99999.90.0340.037
5.21-6.386.29315650.9991000.0360.039
6.38-9.026.07412340.99999.80.0290.032
9.02-47.335.4197140.99998.10.0310.034

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Phasing

PhasingMethod: molecular replacement

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Processing

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

2o02


Resolution: 2.02→47.33 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.929 / SU R Cruickshank DPI: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.138 / SU Rfree Blow DPI: 0.127 / SU Rfree Cruickshank DPI: 0.126
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2098 3.71 %RANDOM
Rwork0.212 ---
obs0.213 56503 99.9 %-
Displacement parametersBiso max: 159.91 Å2 / Biso mean: 63.21 Å2 / Biso min: 39.99 Å2
Baniso -1Baniso -2Baniso -3
1-1.0949 Å20 Å20 Å2
2---11.4562 Å20 Å2
3---10.3614 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: final / Resolution: 2.02→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3769 0 25 236 4030
Biso mean--62.77 68.94 -
Num. residues----471
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1418SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes660HARMONIC5
X-RAY DIFFRACTIONt_it3841HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion495SEMIHARMONIC5
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_contact4506SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3841HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5166HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion2.53
X-RAY DIFFRACTIONt_other_torsion18.72
LS refinement shellResolution: 2.02→2.03 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3089 42 3.71 %
Rwork0.2464 1089 -
all0.2488 1131 -
obs--99.73 %
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)
12.3237-0.26180.7530.8097-0.15822.0711-0.05880.23590.0038-0.00940.0133-0.0237-0.05420.34240.0455-0.6321-0.0920.0102-0.56750.0148-0.625139.1502-2.44927.4535
21.78770.49330.31250.818-0.2451.4629-0.0144-0.1239-0.00870.02760.00750.0532-0.1022-0.01760.0069-0.6105-0.01870.0078-0.58460.0006-0.60824.9058-5.187-9.4572
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 230
2X-RAY DIFFRACTION2{ B|* }B1 - 230

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