PDB-6tjm: Crystal structure of an Estrogen Receptor alpha 8-mer phosphopept...

Basic information

• Entry: Database: PDB / ID: 6tjm
• Title: Crystal structure of an Estrogen Receptor alpha 8-mer phosphopeptide in complex with 14-3-3sigma stabilized by Pyrrolidone1

Components

• 14-3-3 protein sigma
• C-terminal phosphopeptide of human estrogen receptor alpha

• Keywords: SIGNALING PROTEIN / Estrogen receptor / 14-3-3 / PPI / stabiliser / complex

Function / homology

Function:

regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / nuclear estrogen receptor activity / epithelial cell development / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / mammary gland branching involved in pregnancy / regulation of cell-cell adhesion / negative regulation of smooth muscle cell apoptotic process / uterus development / vagina development / TFIIB-class transcription factor binding / steroid hormone receptor signaling pathway / androgen metabolic process / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / Mitochondrial unfolded protein response (UPRmt) / establishment of skin barrier / nuclear receptor-mediated steroid hormone signaling pathway / 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 / Nuclear signaling by ERBB4 / negative regulation of stem cell proliferation / RNA polymerase II preinitiation complex assembly / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of DNA-binding transcription factor activity / negative regulation of protein kinase activity / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / positive regulation of protein localization / protein localization to chromatin / steroid binding / 14-3-3 protein binding / negative regulation of canonical NF-kappaB signal transduction / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / negative regulation of DNA-binding transcription factor activity / positive regulation of cell adhesion / protein sequestering activity / negative regulation of miRNA transcription / nitric-oxide synthase regulator activity / negative regulation of innate immune response / protein export from nucleus / ESR-mediated signaling / TBP-class protein binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / transcription coregulator binding / positive regulation of protein export from nucleus / nuclear estrogen receptor binding / transcription corepressor binding / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / stem cell differentiation / cellular response to estradiol stimulus / SUMOylation of intracellular receptors / euchromatin / transcription coactivator binding / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / nuclear receptor activity / positive regulation of fibroblast proliferation / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / intracellular protein localization / response to estradiol / PIP3 activates AKT signaling / regulation of protein localization / positive regulation of cytosolic calcium ion concentration / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of inflammatory response

Domain/homology:

14-3-3 domain / Delta-Endotoxin; domain 1 / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / 14-3-3 protein sigma / Estrogen receptor/oestrogen-related 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 / 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

Component:

Chem-NE5 / Estrogen receptor / 14-3-3 protein sigma

• Biological species: Homo sapiens (human)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
• Authors: Andrei, S.A. / Bosica, F. / Ottmann, C. / O'Mahony, G.

Funding support

Netherlands, 1items

Organization	Grant number	Country
European Commission		Netherlands

• Citation: Journal: Chemistry / Year: 2020; Title: Design of Drug-Like Protein-Protein Interaction Stabilizers Guided By Chelation-Controlled Bioactive Conformation Stabilization.; Authors: Bosica, F. / Andrei, S.A. / Neves, J.F. / Brandt, P. / Gunnarsson, A. / Landrieu, I. / Ottmann, C. / O'Mahony, G.

History

Deposition	Nov 26, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 29, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jun 10, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Assembly

Deposited unit

A: 14-3-3 protein sigma

B: C-terminal phosphopeptide of human estrogen receptor alpha

hetero molecules

Summary:

• 27.9 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	27,924	4
Polymers	27,440	2
Non-polymers	485	2
Water	2,288	127

1

A: 14-3-3 protein sigma

B: C-terminal phosphopeptide of human estrogen receptor alpha

hetero molecules

A: 14-3-3 protein sigma

B: C-terminal phosphopeptide of human estrogen receptor alpha

hetero molecules

A: 14-3-3 protein sigma

B: C-terminal phosphopeptide of human estrogen receptor alpha

hetero molecules

A: 14-3-3 protein sigma

B: C-terminal phosphopeptide of human estrogen receptor alpha

hetero molecules

Summary:

• defined by software
• Evidence: isothermal titration calorimetry
• 112 kDa, 8 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	111,698	16
Polymers	109,759	8
Non-polymers	1,939	8
Water	144	8

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_655	-x+1,-y,z	1
crystal symmetry operation	3_656	-x+1,y,-z+1	1
crystal symmetry operation	4_556	x,-y,-z+1	1

Calculated values:

Buried area	10230 Å2
ΔGint	-102 kcal/mol
Surface area	41920 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	62.841, 152.310, 76.792
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	21
Space group name H-M	C222

Components on special symmetry positions

ID	Model	Components
1	1	A-514- HOH

Components

#1: Protein

A 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin

Details:

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

B C-terminal phosphopeptide of human estrogen receptor alpha

Details:

Mass: 896.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P03372*PLUS

#3: Chemical

A-301 ChemComp-MG / MAGNESIUM ION

Details:

Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

#4: Chemical

A-302 ChemComp-NE5 / 5-[(2~{R})-2-(4-nitrophenyl)-4-oxidanyl-5-oxidanylidene-3-(phenylcarbonyl)-2~{H}-pyrrol-1-yl]-2-oxidanyl-benzoic acid

Details:

Mass: 460.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₄H₁₆N₂O₈ / Feature type: SUBJECT OF INVESTIGATION

#5: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H₂O

• Has ligand of interest: Y
• Has protein modification: Y

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 3.35 ų/Da / Density % sol: 63.3 %
• Crystal grow: Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 ; Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris, pH 7.0, 10 % v/v PEG 8000

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
• Detector: Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 14, 2018
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1.0332 Å / Relative weight: 1
• Reflection: Resolution: 1.85→76.78 Å / Num. obs: 31900 / % possible obs: 100 % / Redundancy: 12.5 % / CC_1/2: 1 / R_merge(I) obs: 0.043 / R_pim(I) all: 0.013 / R_rim(I) all: 0.045 / Net I/σ(I): 24 / Num. measured all: 398455 / Scaling rejects: 607

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Rmerge(I) obs	Num. measured all	Num. unique obs	CC1/2	Rpim(I) all	Rrim(I) all	Net I/σ(I) obs	% possible all
1.85-1.9	11.5	1.259	26753	2329	0.803	0.386	1.317	1	100
8.27-76.78	11.9	0.023	4860	409	0.998	0.007	0.024	89.5	98.2

Processing

Software

Name	Version	Classification
PHENIX	3500	refinement
xia2		data scaling
PDB_EXTRACT	3.25	data extraction
xia2		data reduction
PHASER	2.8.3	phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JC3

4jc3

Resolution: 1.85→76.155 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.56

	Rfactor	Num. reflection	% reflection
Rfree	0.218	1583	4.96 %
Rwork	0.197	-	-
obs	0.198	31888	99.89 %

• Solvent computation: Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
• Displacement parameters: B_iso max: 199.68 Ų / B_iso mean: 62.1073 Ų / B_iso min: 29.85 Ų

Refinement step

Cycle: final / Resolution: 1.85→76.155 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1844	0	50	127	2021
Biso mean	-	-	51.18	54.19	-
Num. residues	-	-	-	-	234

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	% reflection obs (%)
1.85-1.9096	0.3886	137	0.3491	2727	99
1.9096-1.9779	0.2854	146	0.2756	2707	100
1.9779-2.0571	0.2221	135	0.2285	2714	100
2.0571-2.1507	0.2387	125	0.2081	2730	100
2.1507-2.2641	0.2223	138	0.2065	2746	100
2.2641-2.4059	0.2245	133	0.2103	2758	100
2.4059-2.5917	0.2523	148	0.2213	2714	100
2.5917-2.8525	0.2236	152	0.2334	2762	100
2.8525-3.2653	0.2696	147	0.2205	2756	100
3.2653-4.1139	0.2056	172	0.1829	2775	100
4.1139-76.155	0.1833	150	0.1642	2916	100

Refinement TLS params.

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

ID	L11 (°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)
1	4.2208	1.5061	0.1816	4.6062	-2.1534	5.7325	-0.197	0.0447	-0.0547	-0.2103	0.0401	-0.153	-0.1167	0.1222	0.1438	0.3952	-0.0636	0.0096	0.2387	-0.042	0.3787	39.6262	29.3544	24.1989
2	2.993	0.2201	-3.5416	1.2992	-0.2056	6.5463	-0.2653	0.3357	-0.0756	-0.0707	0.0593	0.1173	-0.091	-0.5304	0.3096	0.3327	-0.0332	-0.0495	0.3132	-0.0569	0.3885	20.9108	25.7945	31.8586
3	7.9071	1.423	-3.3255	4.4354	-0.0803	7.7471	-0.25	1.0316	-0.0702	-0.5118	-0.0053	0.14	-0.3418	-0.8963	0.2289	0.4174	-0.0409	-0.0831	0.5401	-0.0339	0.3554	21.3723	25.5396	16.5633
4	8.3243	-3.494	-3.7752	6.6617	2.9777	2.2303	-0.0277	0.8188	0.1889	-0.6552	-0.5814	0.7849	-0.5869	-1.8085	0.4928	0.4544	0.0129	-0.2034	0.8759	-0.0508	0.4654	14.9872	22.433	11.9456
5	1.8595	-1.808	-0.78	3.3825	0.9327	2.9656	0.1063	0.0104	-0.3152	0.0012	-0.3589	0.4628	0.462	-0.7574	0.1905	0.4558	-0.261	-0.0121	0.5757	-0.1076	0.3898	19.7596	8.0635	14.6833
6	7.8186	1.701	7.205	2.1792	2.7105	7.5244	0.0592	-0.9794	0.7587	0.3022	0.1438	-0.0723	-0.0844	-0.4743	-0.0051	0.5485	-0.1575	-0.0081	0.6394	-0.1021	0.4798	19.5215	13.0806	25.5251

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -4 through 37 )	A	-4 - 37
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 38 through 106 )	A	38 - 106
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 107 through 139 )	A	107 - 139
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 140 through 161 )	A	140 - 161
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 162 through 231 )	A	162 - 231
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 591 through 595 )	B	591 - 595