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- PDB-7pwz: Crystal structure of 14-3-3 sigma in complex with a C-terminal Es... -

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Basic information

Entry
Database: PDB / ID: 7pwz
TitleCrystal structure of 14-3-3 sigma in complex with a C-terminal Estrogen Receptoralpha phosphopeptide, stabilised by Pyrrolidone1 derivative 228
Components
  • 14-3-3 protein sigma
  • C-terminus of Estrogen receptor alpha
KeywordsCHAPERONE / Nuclear receptor / phosphorylation / trafficking / PPI stabiliser
Function / homology
Function and homology information


regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / negative regulation of keratinocyte proliferation ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / negative regulation of keratinocyte proliferation / Activation of BAD and translocation to mitochondria / establishment of skin barrier / negative regulation of protein localization to plasma membrane / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / RHO GTPases activate PKNs / negative regulation of innate immune response / protein sequestering activity / protein kinase A signaling / protein export from nucleus / positive regulation of cell adhesion / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / regulation of protein localization / positive regulation of cell growth / regulation of cell cycle / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Chem-8CQ / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsAndrei, S.A. / Bosica, F. / O'Mahony, G. / Ottmann, C.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission675179 Netherlands
Netherlands Organisation for Scientific Research (NWO)717.014.001 Netherlands
CitationJournal: J.Med.Chem. / Year: 2022
Title: Designing Selective Drug-like Molecular Glues for the Glucocorticoid Receptor/14-3-3 Protein-Protein Interaction.
Authors: Pallesen, J.S. / Munier, C.C. / Bosica, F. / Andrei, S.A. / Edman, K. / Gunnarsson, A. / La Sala, G. / Putra, O.D. / Srdanovic, S. / Wilson, A.J. / Wissler, L. / Ottmann, C. / Perry, M.W.D. / O'Mahony, G.
History
DepositionOct 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: C-terminus of Estrogen receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9094
Polymers27,4142
Non-polymers4962
Water3,351186
1
A: 14-3-3 protein sigma
B: C-terminus of Estrogen receptor alpha
hetero molecules

A: 14-3-3 protein sigma
B: C-terminus of Estrogen receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8198
Polymers54,8284
Non-polymers9914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area4030 Å2
ΔGint-43 kcal/mol
Surface area22170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.173, 151.615, 78.945
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-621-

HOH

21A-663-

HOH

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Components

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


Mass: 26542.914 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 C-terminus of Estrogen receptor alpha


Mass: 870.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-8CQ / 2-oxidanyl-5-[(2~{R})-4-oxidanyl-5-oxidanylidene-2-(1-oxidanylidene-3~{H}-2-benzofuran-5-yl)-3-(phenylcarbonyl)-2~{H}-pyrrol-1-yl]benzoic acid


Mass: 471.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H17NO8 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 3.5 Å3/Da / Density % sol: 64.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1 : 1 (v/v) 0.1 M Tris, pH 7.0, 0.2 magnesium chloride hexahydrate and 10 % v/v PEG 8000

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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 300K / Detector: PIXEL / Date: Jun 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.5→29.73 Å / Num. obs: 13499 / % possible obs: 98.4 % / Redundancy: 6 % / Biso Wilson estimate: 38.03 Å2 / Rpim(I) all: 0.071 / Rrim(I) all: 0.177 / Net I/σ(I): 6 / Num. measured all: 80982
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
2.5-2.546.21.738326190.2710.68192.1
6.76-29.7359.138107570.0210.04999.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.89 Å29.73 Å
Translation4.89 Å29.73 Å

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Processing

Software
NameVersionClassification
PHENIX2.8.3refinement
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JC3

4jc3


Resolution: 2.5→29.73 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.298 651 4.83 %
Rwork0.244 12827 -
obs0.2466 13478 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.65 Å2 / Biso mean: 47.5355 Å2 / Biso min: 19.39 Å2
Refinement stepCycle: final / Resolution: 2.5→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 52 186 2051
Biso mean--33.89 41.87 -
Num. residues----231
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.690.34711240.31492497262198
2.69-2.960.40781230.331225792702100
2.96-3.390.31551490.273625692718100
3.39-4.270.27691040.21662499260395
4.27-29.730.25561510.2062683283499
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)
13.065-0.9401-0.66551.3634-2.17185.6902-0.09320.23680.0163-0.17130.10220.07840.379-0.13380.00850.3046-0.0986-0.03650.1834-0.02040.328140.499128.984125.39
26.5074-0.8125-6.72771.16610.56817.422-0.80460.8356-0.8009-0.08560.07310.11910.6856-0.82380.68540.332-0.0988-0.03320.2765-0.07120.290424.371721.596931.2488
34.24080.9492-5.97881.4044-0.92099.2892-0.17030.51220.1820.10780.1492-0.0023-0.2123-0.61580.01340.23870.0075-0.09740.28490.04590.388218.882930.641434.5075
44.01880.4398-3.21143.2965-0.4487.2956-0.25761.2183-0.192-0.46780.08980.07660.2742-1.10250.1080.4123-0.2259-0.11320.60070.04830.306722.384624.782318.3849
53.588-0.6387-0.35712.6599-0.08681.8381-0.26890.54180.3064-0.31390.0530.24590.1392-1.12470.20960.5296-0.3093-0.14450.90850.02680.394817.213818.944414.5457
62.68311.71571.25064.87141.14691.62090.2481-0.2056-0.13910.28320.02270.64460.2022-0.4151-0.04130.7277-0.7847-0.15640.8984-0.1140.372714.73036.486512.7063
73.0433-2.5672-1.91542.80480.32513.58580.09430.1961-0.24620.0001-0.39070.23120.4437-0.41790.26980.7626-0.33910.01310.4888-0.05820.336325.62324.444315.6341
83.5173-0.78714.37078.88071.05685.89910.4506-1.67390.14310.8428-0.07310.573-0.0732-0.0407-0.35610.5271-0.31290.05190.7008-0.00890.385120.355712.957226.2498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 37 )A-4 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 68 )A38 - 68
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 106 )A69 - 106
4X-RAY DIFFRACTION4chain 'A' and (resid 107 through 137 )A107 - 137
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 184 )A138 - 184
6X-RAY DIFFRACTION6chain 'A' and (resid 185 through 203 )A185 - 203
7X-RAY DIFFRACTION7chain 'A' and (resid 204 through 231 )A204 - 231
8X-RAY DIFFRACTION8chain 'B' and (resid 591 through 595 )B591 - 595

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