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- PDB-5wgd: Estrogen Receptor Alpha Ligand Binding Domain in Complex with Est... -

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Basic information

Entry
Database: PDB / ID: 5wgd
TitleEstrogen Receptor Alpha Ligand Binding Domain in Complex with Estradiol and SRC2-LP1
Components
  • (ACE)AILHKLLQDS(NH2)
  • (ACE)HKILHKLLQDS(NH2)
  • Estrogen receptor
KeywordsTRANSCRIPTION / Breast Cancer / Stapled Peptides / Synthetic Peptides / Hormone
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / 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 / steroid hormone receptor signaling pathway / epithelial cell proliferation involved in mammary gland duct elongation ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / 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 / steroid hormone receptor signaling pathway / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / mammary gland branching involved in pregnancy / uterus development / negative regulation of smooth muscle cell apoptotic process / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / : / : / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / protein localization to chromatin / steroid binding / 14-3-3 protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / negative regulation of canonical NF-kappaB signal transduction / ESR-mediated signaling / negative regulation of miRNA transcription / TBP-class protein binding / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / transcription corepressor binding / transcription coregulator binding / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / transcription coactivator binding / male gonad development / nuclear receptor activity / positive regulation of fibroblast proliferation / Constitutive Signaling by Aberrant PI3K in Cancer / sequence-specific double-stranded DNA binding / Regulation of RUNX2 expression and activity / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / response to estradiol / PIP3 activates AKT signaling / positive regulation of cytosolic calcium ion concentration / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / DNA-binding transcription activator activity, RNA polymerase II-specific / fibroblast proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / calmodulin binding / Extra-nuclear estrogen signaling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor ...Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ESTRADIOL / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFanning, S.W. / Speltz, T.E. / Mayne, C.G. / Siddiqui, Z. / Greene, G.L. / Tajkhorshid, E. / Moore, T.W.
CitationJournal: Org. Biomol. Chem. / Year: 2018
Title: A "cross-stitched" peptide with improved helicity and proteolytic stability.
Authors: Speltz, T.E. / Mayne, C.G. / Fanning, S.W. / Siddiqui, Z. / Tajkhorshid, E. / Greene, G.L. / Moore, T.W.
History
DepositionJul 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Advisory / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Revision 1.2Oct 4, 2023Group: 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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
E: (ACE)HKILHKLLQDS(NH2)
F: (ACE)AILHKLLQDS(NH2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6166
Polymers62,0714
Non-polymers5452
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-36 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.037, 83.831, 58.375
Angle α, β, γ (deg.)90.00, 108.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 29774.123 Da / Num. of mol.: 2 / Mutation: Y364S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03372
#2: Protein/peptide (ACE)HKILHKLLQDS(NH2)


Mass: 1359.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide (ACE)AILHKLLQDS(NH2)


Mass: 1163.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-EST / ESTRADIOL


Mass: 272.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3,350, MgCl2, Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 45402 / % possible obs: 96.4 % / Redundancy: 3.6 % / Net I/σ(I): 19.2
Reflection shellResolution: 1.8→1.83 Å / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DXE

5dxe


Resolution: 1.8→26.6 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.74
RfactorNum. reflection% reflection
Rfree0.208 2083 4.88 %
Rwork0.176 --
obs0.177 42687 90.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→26.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3681 0 40 416 4137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063856
X-RAY DIFFRACTIONf_angle_d1.2945234
X-RAY DIFFRACTIONf_dihedral_angle_d13.7671476
X-RAY DIFFRACTIONf_chiral_restr0.087629
X-RAY DIFFRACTIONf_plane_restr0.004647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8038-1.84570.3654640.26741358X-RAY DIFFRACTION46
1.8457-1.89180.2929990.26011979X-RAY DIFFRACTION66
1.8918-1.9430.26351360.22662529X-RAY DIFFRACTION84
1.943-2.00010.25861660.20662721X-RAY DIFFRACTION93
2.0001-2.06470.26421390.20122804X-RAY DIFFRACTION95
2.0647-2.13840.20861410.18372846X-RAY DIFFRACTION95
2.1384-2.2240.20881490.16952885X-RAY DIFFRACTION96
2.224-2.32520.20551610.17452883X-RAY DIFFRACTION97
2.3252-2.44770.19641260.17472938X-RAY DIFFRACTION98
2.4477-2.60090.23561690.17612913X-RAY DIFFRACTION98
2.6009-2.80150.251440.18722980X-RAY DIFFRACTION99
2.8015-3.08310.20941480.17442943X-RAY DIFFRACTION98
3.0831-3.52830.19511450.16472969X-RAY DIFFRACTION99
3.5283-4.4420.16781620.14352961X-RAY DIFFRACTION99
4.442-26.60190.1861340.17772895X-RAY DIFFRACTION94
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)
13.77850.68970.33643.8852-1.92294.04910.36430.89721.0373-0.3650.2010.8095-0.4646-0.5116-0.26430.2710.0096-0.06290.31980.14820.330537.93599.812750.8525
27.0034-5.65162.53736.676-1.64721.760.03010.10910.3198-0.2750.0131-0.65340.13540.0044-0.0020.1760.00080.0520.1958-0.01880.20864.9234-6.826551.4401
36.4524-4.8661.06695.7644-1.21970.86510.23940.2826-0.0263-0.4382-0.1552-0.1524-0.01980.2234-0.05410.1368-0.01940.02610.1519-0.01380.096561.85092.490556.0915
41.65120.3611-0.09195.34520.61791.92230.0404-0.02120.22470.0183-0.00550.1983-0.20850.0385-0.03390.0742-0.01170.03120.10910.00590.082352.83249.275261.2977
52.2810.5533-0.44353.98-0.42072.8338-0.1880.1295-0.6861-0.4005-0.10220.1810.47560.10860.06540.17370.00330.03740.1063-0.05390.221855.2121-11.973655.4434
61.9465-0.66933.60611.4872-1.25778.66860.1104-0.0592-0.5305-0.05540.2103-0.03150.5160.0989-0.25390.27070.04920.08660.1530.03830.28663.732-14.646163.1754
72.1079-0.3511.44113.2734-0.34743.2934-0.1664-0.1927-0.72250.17240.00320.35950.1650.0110.11470.16870.00110.04560.11580.00780.207351.2345-10.841365.4097
84.99881.30680.47912.71570.60292.53170.06340.00250.07170.025-0.11170.0877-0.1468-0.24510.10050.09610.0070.01290.12630.03210.084844.15554.740161.4634
95.98571.2586-0.37072.8486-0.14642.74090.06850.43050.3798-0.3535-0.0993-0.0147-0.3724-0.2602-0.03760.1410.060.00120.25170.04910.139134.03136.530560.1066
105.6956-0.3538-0.29440.6980.17590.2016-0.134-0.1725-0.09990.03390.0801-0.02310.02850.05640.03260.12380.0020.01550.14560.00880.07549.1241-1.442469.1733
117.633-5.01972.98353.5546-1.14314.31710.60660.1831-0.347-0.28970.02160.12740.29840.0848-0.23770.109-0.0119-0.020.2104-0.00020.260873.94240.580165.4339
128.5588-3.1488-1.74052.9089-0.3187.08220.048-0.33770.42320.29450.0041-0.4403-0.47780.2129-0.16260.1875-0.01920.00530.1660.01620.319265.6389.615965.6502
134.0818-0.41062.5621.9652-0.83253.8125-0.0434-0.8241-0.64130.46180.22910.51380.0241-0.7569-0.3410.23690.05010.05020.32750.07040.185732.0578-1.162489.4415
144.96431.67933.20093.86650.85643.9268-0.27490.01420.15010.51790.1135-0.2077-0.13260.19890.08820.25930.0429-0.03740.1523-0.00240.116348.53210.401794.9538
158.588-6.5876-1.84875.06041.53142.7122-0.2705-0.0387-1.3575-0.23890.15760.93070.4756-0.550.13650.3695-0.0749-0.06040.21170.03860.357636.7777-14.040984.7976
162.7527-0.79520.42155.18560.26223.36880.03350.0129-0.15790.2044-0.0116-0.20560.09870.1777-0.02380.10980.0072-0.01880.13660.00070.062945.9471-2.99185.2791
172.5461-0.70281.07431.7748-0.93180.745-0.3737-0.43380.77740.94270.3112-0.0954-0.9604-0.23260.31650.59960.0852-0.11290.0274-0.13950.159144.162315.372791.5989
182.9425-2.9952-1.4813.68191.01952.1806-0.2003-0.08970.82380.18570.0461-1.1086-0.8830.40680.06620.5787-0.12-0.24570.2429-0.03660.441655.722117.143990.705
197.1990.083.36165.27850.12765.0152-0.1981-0.02590.28650.079-0.0149-0.1342-0.64520.03850.21710.2916-0.0301-0.01670.1252-0.00350.140546.655614.309381.1188
204.054-1.44090.06577.22990.9375.03390.02320.1727-0.2014-0.1443-0.14610.1184-0.0248-0.0290.19060.1118-0.0221-0.00630.13470.0030.07137.9276-0.891679.4853
217.2562-5.17751.02026.3382-1.41573.3621-0.0256-0.1181-0.35170.0207-0.0850.29230.2032-0.12680.12060.0836-0.03210.01680.21640.00640.148928.6425-1.891274.98
222.9808-0.27912.47022.2803-0.88874.6842-0.13170.22140.3550.0425-0.0733-0.2553-0.14240.4190.12980.1231-0.02640.03890.1083-0.01980.081946.46754.819276.8052
236.9333-0.10141.76460.623-1.07452.2372-0.0762-0.21090.92150.23010.29830.19-0.1520.1420.33720.3736-0.0923-0.24160.522-0.07630.504663.49760.859495.8403
246.92362.09223.75365.0921.66082.16420.151-0.0089-0.7680.3571-0.2376-0.94110.38310.83090.13020.2561-0.0104-0.08030.28260.0330.299356.913-6.980789.2173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 308 THROUGH 321 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 322 THROUGH 338 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 339 THROUGH 363 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 364 THROUGH 394 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 395 THROUGH 407 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 408 THROUGH 420 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 421 THROUGH 438 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 439 THROUGH 473 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 474 THROUGH 496 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 497 THROUGH 530 )
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 531 THROUGH 537 )
12X-RAY DIFFRACTION12CHAIN 'A' AND (RESID 538 THROUGH 547 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 307 THROUGH 338 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 339 THROUGH 363 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 364 THROUGH 371 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 372 THROUGH 394 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 395 THROUGH 407 )
18X-RAY DIFFRACTION18CHAIN 'B' AND (RESID 408 THROUGH 420 )
19X-RAY DIFFRACTION19CHAIN 'B' AND (RESID 421 THROUGH 438 )
20X-RAY DIFFRACTION20CHAIN 'B' AND (RESID 439 THROUGH 473 )
21X-RAY DIFFRACTION21CHAIN 'B' AND (RESID 474 THROUGH 496 )
22X-RAY DIFFRACTION22CHAIN 'B' AND (RESID 497 THROUGH 530 )
23X-RAY DIFFRACTION23CHAIN 'B' AND (RESID 531 THROUGH 537 )
24X-RAY DIFFRACTION24CHAIN 'B' AND (RESID 538 THROUGH 548 )

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