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- PDB-4pp6: Crystal Structure of the Estrogen Receptor alpha Ligand-binding D... -

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Basic information

Entry
Database: PDB / ID: 4pp6
TitleCrystal Structure of the Estrogen Receptor alpha Ligand-binding Domain in Complex with Resveratrol
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsPROTEIN BINDING / nuclear hormone receptor / transcription factor / ligand binding / nucleus
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / epithelial cell development / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / aryl hydrocarbon receptor binding / androgen metabolic process / TFIIB-class transcription factor binding / regulation of lipid metabolic process / steroid hormone mediated signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / positive regulation of phospholipase C activity / intracellular steroid hormone receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / protein localization to chromatin / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / steroid binding / Regulation of lipid metabolism by PPARalpha / nitric-oxide synthase regulator activity / ESR-mediated signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / 14-3-3 protein binding / transcription corepressor binding / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / nuclear receptor coactivator activity / response to progesterone / cellular response to estradiol stimulus / transcription coregulator binding / nuclear estrogen receptor binding / stem cell differentiation / positive regulation of nitric-oxide synthase activity / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / euchromatin / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / nuclear receptor activity / positive regulation of nitric oxide biosynthetic process / positive regulation of DNA-binding transcription factor activity / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / Circadian Clock / sequence-specific double-stranded DNA binding / response to estradiol / PIP3 activates AKT signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / HATs acetylate histones / ATPase binding / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / fibroblast proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
Similarity search - Function
Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 ...Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Nuclear receptor coactivator, interlocking / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / 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
RESVERATROL / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsNwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Parent, A.A. / Hughes, T.S. / Pollock, J.A. / Gjyshi, O. / Cavett, V. / Nowak, J. / Garcia-Ordonez, R.D. ...Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Parent, A.A. / Hughes, T.S. / Pollock, J.A. / Gjyshi, O. / Cavett, V. / Nowak, J. / Garcia-Ordonez, R.D. / Houtman, R. / Griffin, P.R. / Kojetin, D.J. / Katzenellenbogen, J.A. / Conkright, M.D. / Nettles, K.W.
CitationJournal: Elife / Year: 2014
Title: Resveratrol modulates the inflammatory response via an estrogen receptor-signal integration network.
Authors: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Parent, A.A. / Hughes, T.S. / Pollock, J.A. / Gjyshi, O. / Cavett, V. / Nowak, J. / Garcia-Ordonez, R.D. / Houtman, R. / Griffin, P.R. / ...Authors: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Parent, A.A. / Hughes, T.S. / Pollock, J.A. / Gjyshi, O. / Cavett, V. / Nowak, J. / Garcia-Ordonez, R.D. / Houtman, R. / Griffin, P.R. / Kojetin, D.J. / Katzenellenbogen, J.A. / Conkright, M.D. / Nettles, K.W.
History
DepositionFeb 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3996
Polymers57,9424
Non-polymers4562
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-24 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.040, 84.670, 58.420
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 / / Estrogen receptor alpha / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 27832.783 Da / Num. of mol.: 2 / Fragment: ligand-binding domain (UNP residues 305-548) / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR, ESR1, NR3A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03372
#2: Protein/peptide Nuclear receptor coactivator 2 / / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1138.383 Da / Num. of mol.: 2
Fragment: receptor-interacting peptide (UNP residues 688-696)
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-STL / RESVERATROL / Resveratrol


Mass: 228.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 15% PEG3350, 0.05 M magnesium chloride, 0.067 M sodium chloride, 0.1 M Tris, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2009
RadiationMonochromator: Side scattering bent cube I-beam single crystal, asymmetric cut 4.965 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→33.7 Å / Num. all: 22678 / Num. obs: 22678 / % possible obs: 86.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2.9 / Num. unique all: 994 / % possible all: 36.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.automr)model building
PHENIX(phenix.refine: 1.8_1066)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QA8

2qa8


Resolution: 2.201→33.651 Å / SU ML: 0.27 / σ(F): 0 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1077 5.05 %RANDOM
Rwork0.167 ---
all0.1698 22678 --
obs0.1698 21340 81.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.201→33.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3788 0 34 307 4129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083983
X-RAY DIFFRACTIONf_angle_d1.0035403
X-RAY DIFFRACTIONf_dihedral_angle_d14.4691475
X-RAY DIFFRACTIONf_chiral_restr0.066637
X-RAY DIFFRACTIONf_plane_restr0.004672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.201-2.30170.3063580.24391010X-RAY DIFFRACTION33
2.3017-2.4230.3053980.20321806X-RAY DIFFRACTION58
2.423-2.57470.24951310.17912539X-RAY DIFFRACTION81
2.5747-2.77340.26931460.17422781X-RAY DIFFRACTION90
2.7734-3.05240.20951540.16322956X-RAY DIFFRACTION95
3.0524-3.49370.21991620.15693025X-RAY DIFFRACTION97
3.4937-4.40010.17931610.14113052X-RAY DIFFRACTION98
4.4001-33.6550.20841670.17643094X-RAY DIFFRACTION97
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)
14.0612-1.62991.17131.9206-0.01431.78450.42420.46570.1268-0.1980.00950.21650.0043-0.3705-0.04090.18950.0656-0.0110.25260.10170.18762.773927.3962-5.3913
21.7718-0.63681.02621.8506-0.872.55260.1040.26090.1121-0.2622-0.2362-0.50090.27740.0380.06130.23310.05460.07380.20.03880.267830.977610.6505-0.8476
30.9410.1559-0.35052.13940.0361.25990.12740.04780.2515-0.21960.03950.1211-0.1740.0691-0.06030.14230.01290.02220.11960.01620.172717.024326.37532.9452
42.2916-0.5307-0.71021.974-0.1820.6759-0.0976-0.0815-0.4422-0.1145-0.0196-0.17440.35770.02860.05130.2008-0.00230.00190.130.00140.177420.11056.94077.2219
52.28490.6137-0.42292.0302-0.361.15960.06120.24210.1709-0.173-0.04750.1599-0.0724-0.15360.0470.13070.0268-0.02290.1768-0.01230.10810.288122.94656.5814
61.8313-1.2568-0.55180.86970.37470.17370.0875-0.22680.2606-0.0305-0.0092-0.3265-0.14020.1219-0.0310.1389-0.0024-0.02590.1688-0.00110.202424.943521.477212.8998
72.97620.48561.79532.61791.2034.00420.1924-0.2740.0230.6113-0.15330.25590.0377-0.30540.00950.2902-0.02890.06030.24870.02850.178-4.243719.357535.2703
81.63680.47670.7271.34631.83022.4923-0.05230.00680.22320.3064-0.3344-0.186-0.44270.2346-0.40510.4206-0.1126-0.15810.2670.05170.216716.946925.456641.3065
91.19070.00270.21631.9895-0.21811.82240.0436-0.08070.02320.4134-0.0615-0.0192-0.19330.02360.02440.19970.0102-0.02130.11810.00150.09077.930721.404932.8075
102.37090.0209-0.01722.5170.11291.3571-0.0517-0.0903-0.007-0.1861-0.06580.1198-0.08460.02380.08860.1390.0093-0.0010.1593-0.00380.05383.392522.014723.626
111.6499-0.03140.44591.4508-0.09910.81590.0585-0.10760.15330.0111-0.03670.1318-0.151-0.06970.02530.0947-0.02250.02360.1563-0.02780.1305-0.644623.837719.1003
122.03691.30261.1061.79790.41872.99020.2933-0.0642-0.06270.3998-0.3796-0.45620.10131.2219-0.16610.329-0.0551-0.04060.4310.01780.226623.03816.748535.5506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 309:324)
2X-RAY DIFFRACTION2(chain A and resid 325:345)
3X-RAY DIFFRACTION3(chain A and resid 346:397)
4X-RAY DIFFRACTION4(chain A and resid 398:436)
5X-RAY DIFFRACTION5(chain A and resid 437:508)
6X-RAY DIFFRACTION6(chain A and resid 509:547)
7X-RAY DIFFRACTION7(chain B and resid 308:332)
8X-RAY DIFFRACTION8(chain B and resid 337:354)
9X-RAY DIFFRACTION9(chain B and resid 355:420)
10X-RAY DIFFRACTION10(chain B and resid 421:479)
11X-RAY DIFFRACTION11(chain B and resid 480:525)
12X-RAY DIFFRACTION12(chain B and resid 526:547)

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