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

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Basic information

Entry
Database: PDB / ID: 7pwt
TitleCrystal structure of 14-3-3 sigma in complex with a C-terminal Estrogen Receptor alpha phosphopeptide, stabilised by pyrrolidone 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 / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / 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 protein kinase activity / 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 cell adhesion / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / intrinsic apoptotic signaling pathway in response to DNA damage / intracellular 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 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 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
Chem-PJN / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.312 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
Revision 1.3Oct 9, 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 sigma
B: C-terminus of Estrogen receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8544
Polymers27,4142
Non-polymers4412
Water3,909217
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)55,7098
Polymers54,8284
Non-polymers8814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area4050 Å2
ΔGint-40 kcal/mol
Surface area22060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.838, 151.081, 77.721
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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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: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PJN / (2~{R})-1-(2-hydroxyphenyl)-2-(4-nitrophenyl)-4-oxidanyl-3-(phenylcarbonyl)-2~{H}-pyrrol-5-one


Mass: 416.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H16N2O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3.51 Å3/Da / Density % sol: 65 %
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: 1.5419 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.31→29.53 Å / Num. obs: 16214 / % possible obs: 96.1 % / Redundancy: 5.6 % / CC1/2: 0.982 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.07 / Rrim(I) all: 0.176 / Net I/σ(I): 5.5
Reflection shellResolution: 2.31→2.35 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.792 / Num. unique obs: 551 / CC1/2: 0.881 / Rpim(I) all: 0.429 / Rrim(I) all: 0.907

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.9 Å29.53 Å
Translation4.9 Å29.53 Å

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Processing

Software
NameVersionClassification
PHENIX3500refinement
Aimlessdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JC3

4jc3


Resolution: 2.312→29.526 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2535 771 4.83 %
Rwork0.228 15206 -
obs0.2293 15977 94.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.96 Å2 / Biso mean: 52.6796 Å2 / Biso min: 12.93 Å2
Refinement stepCycle: final / Resolution: 2.312→29.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 48 218 2092
Biso mean--83.55 45.69 -
Num. residues----232
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3123-2.45710.39191240.4029207179
2.4571-2.64670.29011130.3114262799
2.6467-2.91280.27221380.2734262399
2.9128-3.33380.27521340.2409260599
3.3338-4.19830.24791280.1945257095
4.1983-29.520.20171340.185271097
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)
12.1856-1.0767-0.42833.62930.88083.4823-0.04990.3694-0.0903-0.0893-0.23480.4330.488-1.04810.22470.4239-0.2381-0.02890.6583-0.07560.306718.869412.269814.5058
21.99637.43195.04912.0274-1.684.11460.8973-1.1802-0.10131.4582-0.27210.02720.06760.1439-0.27950.4566-0.22390.01650.5518-0.09170.376920.048813.117325.7761
34.2653-0.2169-0.37964.3227-3.25229.2903-0.13180.2153-0.117-0.15560.16230.01520.11750.0043-0.0270.2475-0.0850.02120.1904-0.06470.282640.085529.239124.2912
45.1497-0.4373-3.51790.90650.38343.7232-0.30540.5072-0.2551-0.05410.0150.04210.1085-0.59560.32260.2664-0.0401-0.04470.2522-0.04080.262621.522225.822832.406
55.06660.2583-2.46445.49641.03638.3334-0.32271.0185-0.0382-0.46820.0447-0.1457-0.3105-0.67030.34120.3818-0.113-0.09220.46820.00220.276923.024925.417617.2466
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 137 through 231 )A137 - 231
2X-RAY DIFFRACTION2chain 'B' and (resid 591 through 595 )B591 - 595
3X-RAY DIFFRACTION3chain 'A' and (resid -4 through 37 )A-4 - 37
4X-RAY DIFFRACTION4chain 'A' and (resid 38 through 105 )A38 - 105
5X-RAY DIFFRACTION5chain 'A' and (resid 106 through 136 )A106 - 136

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