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- PDB-4zn7: Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) i... -

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Basic information

Entry
Database: PDB / ID: 4zn7
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in complex with Diethylstilbestrol
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION / Nuclear receptor Transcription factor Nucleus protein-ligand complex
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / 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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / prostate epithelial cord elongation / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / regulation of lipid metabolic process / androgen metabolic process / steroid hormone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / estrogen receptor signaling pathway / cellular response to estrogen stimulus / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / estrogen response element binding / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / : / nuclear receptor-mediated steroid hormone 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 / 14-3-3 protein binding / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / TBP-class protein binding / nitric-oxide synthase regulator activity / steroid binding / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / BMAL1:CLOCK,NPAS2 activates circadian gene expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / response to progesterone / stem cell differentiation / nuclear estrogen receptor binding / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / euchromatin / 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 / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / HATs acetylate histones / positive regulation of cytosolic calcium ion concentration / ATPase binding / 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 / Nuclear receptor coactivator, interlocking / 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. / 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
DIETHYLSTILBESTROL / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.934 Å
AuthorsNwachukwu, J.C. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Cavett, V. / Nowak, J. / Houtman, R. ...Nwachukwu, J.C. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Cavett, V. / Nowak, J. / Houtman, R. / Carlson, K.E. / Josan, J.S. / Elemento, O. / Katzenellenbogen, J.A. / Zhou, H.B. / Nettles, K.W.
CitationJournal: Mol.Syst.Biol. / Year: 2016
Title: Predictive features of ligand-specific signaling through the estrogen receptor.
Authors: Nwachukwu, J.C. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Nowak, J. / Wright, N.J. / Houtman, R. / Carlson, K.E. / Josan, J.S. / Elemento, O. / ...Authors: Nwachukwu, J.C. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Nowak, J. / Wright, N.J. / Houtman, R. / Carlson, K.E. / Josan, J.S. / Elemento, O. / Katzenellenbogen, J.A. / Zhou, H.B. / Nettles, K.W.
History
DepositionMay 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)62,3556
Polymers61,8194
Non-polymers5372
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-34 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.700, 81.560, 58.300
Angle α, β, γ (deg.)90.000, 111.040, 90.000
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: 29329.457 Da / Num. of mol.: 2 / Fragment: ligand-binding domain, UNP residues 301-559 / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: 1579.866 Da / Num. of mol.: 2
Fragment: Nuclear receptor-interacting peptide, UNP residues 686-698
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-DES / DIETHYLSTILBESTROL


Mass: 268.350 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20O2 / Comment: medication, hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 15% PEG 3350, 0.05M MgCl2, 0.067M NaCl, 0.1M Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 0.9 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.93→40.78 Å / Num. obs: 35338 / % possible obs: 98.82 % / Redundancy: 4.4 % / Net I/σ(I): 5.3
Reflection shellResolution: 1.93→2 Å / Mean I/σ(I) obs: 3.9 / % possible all: 88.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B1V

2b1v


Resolution: 1.934→40.78 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2262 1756 4.97 %
Rwork0.1972 33563 -
obs0.1987 35319 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.44 Å2 / Biso mean: 44.4111 Å2 / Biso min: 13.78 Å2
Refinement stepCycle: final / Resolution: 1.934→40.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3879 0 40 240 4159
Biso mean--35.06 43.09 -
Num. residues----490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044007
X-RAY DIFFRACTIONf_angle_d0.7565420
X-RAY DIFFRACTIONf_chiral_restr0.028636
X-RAY DIFFRACTIONf_plane_restr0.005675
X-RAY DIFFRACTIONf_dihedral_angle_d13.0921480
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.934-1.98630.34711180.3005219985
1.9863-2.04480.33291480.28259599
2.0448-2.11080.31661250.27962596100
2.1108-2.18620.28561300.24872609100
2.1862-2.27370.33431130.25562629100
2.2737-2.37720.24081410.23252603100
2.3772-2.50250.26431410.21382571100
2.5025-2.65930.2561440.21772626100
2.6593-2.86460.27371500.21592586100
2.8646-3.15270.21861530.19852608100
3.1527-3.60870.22671410.18252616100
3.6087-4.54560.16361250.15482648100
4.54560.17121270.1682677100
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)
13.70430.6159-1.28463.18930.21622.9927-0.19680.33960.0725-0.28540.0168-0.1823-0.1060.03380.03770.294-0.0370.0330.3446-0.00270.254421.01775.064-7.9033
22.28310.466-1.48592.6137-0.71055.0161-0.22460.1376-0.3322-0.13720.0536-0.00060.6865-0.14460.08840.2803-0.00610.01180.2026-0.0290.208314.4961-1.5833-4.2197
34.28110.0853-1.45035.69550.68846.3666-0.0540.42770.2085-0.55680.31150.0482-1.406-0.2925-0.1490.4551-0.014-0.0020.31860.02930.288911.908216.9408-6.6662
46.32841.971-2.75481.30190.08312.6096-0.11310.46720.20330.09580.39031.0529-1.0058-1.171-0.33430.55720.23790.10360.78010.28340.62611.211813.9472-8.8426
52.18441.20032.18972.1897-0.61576.51180.067-0.18240.55340.34370.17980.4495-1.7669-0.51530.02940.4530.12850.12850.29030.0580.39758.464815.04962.1491
62.34840.07740.88193.87360.63215.76920.1293-0.1488-0.11350.2902-0.3014-0.09190.2710.81460.15020.2498-0.0148-0.00090.41890.06580.258724.79663.10588.3022
75.89941.74362.01652.69690.46465.7846-0.1154-0.06240.11590.0002-0.01920.2096-0.3024-0.06430.20180.1820.01390.03010.17720.0020.206410.52526.52977.1186
83.89260.3107-1.20833.87841.81434.0433-0.29170.3139-0.22950.25250.01640.54870.3225-2.04590.34370.5892-0.11240.06480.6763-0.08420.59292.3355-6.9072-6.1617
92.97310.5692-1.01072.9568-0.97140.5083-0.181-0.59410.67570.0830.23010.1018-0.91371.21640.22270.7662-0.4316-0.04570.6459-0.09580.448215.499917.384932.2376
102.68834.02561.13486.98291.19062.52090.0756-0.39070.0010.608-0.33050.92890.8109-0.01650.23710.4746-0.02570.14610.386-0.03330.5283-4.4819-8.133634.201
114.67532.3453-1.90034.3787-2.52192.384-0.0424-0.152-0.1598-0.25880.09910.0024-0.341-0.1364-0.01660.2830.00280.03620.2673-0.0160.2931-3.87062.244628.2539
123.0635-0.5009-1.06564.3646-0.92354.04580.2343-0.02140.48840.326-0.1409-0.0477-0.66270.0388-0.08110.227-0.04760.04290.2465-0.03270.28263.292710.744222.6171
133.4328-0.8419-1.27574.3019-0.45066.1571-0.2605-0.4038-0.51060.3256-0.2117-0.20940.28570.39560.21140.33770.0703-0.00270.3340.08970.30526.6783-9.331730.7197
145.7918-1.33692.16461.5478-0.13865.80740.46890.183-1.5097-0.39020.08860.63011.87680.01750.36080.7779-0.04650.14630.25240.06190.7077-0.996-15.093922.7031
157.89650.74950.61544.2182-0.25563.93360.0484-0.0676-0.9776-0.1343-0.1243-0.15630.58310.16580.14050.42080.01540.05660.20580.00990.31859.4912-8.812920.3012
164.6697-0.1971-0.99984.0280.24643.92830.1454-0.3840.02810.517-0.2011-0.2489-0.24250.58530.06510.2978-0.1291-0.02330.3495-0.01610.233914.50435.843625.4473
172.7612-0.15542.13669.4072-3.93793.19790.36711.08370.6301-1.1305-0.1518-0.5698-1.07650.3033-0.35960.78950.03790.17630.60170.06850.49366.654516.192612.2313
187.23330.88250.29861.5550.96224.49510.9385-0.48730.80160.7502-0.69750.174-0.91130.36091.21750.724-0.4557-0.0710.4691-0.17060.215820.949814.100723.7544
196.54030.8562-0.81981.6752-0.12712.5660.4291-0.0139-0.12230.0895-0.32-0.00750.25260.0601-0.14170.2956-0.0115-0.03370.21950.00270.20139.66510.657815.8295
203.5666-0.7876-1.26671.99940.43785.2682-0.25040.450.0346-0.3170.01590.46560.9315-0.8671-0.01970.3151-0.02520.08870.3882-0.05740.4844-10.93313.577318.5826
210.22440.1201-0.06450.21710.17530.5304-0.50070.5339-1.007-0.4170.00390.01511.12140.2448-0.1630.81240.04940.04750.3813-0.05820.503416.0659-14.347-7.8121
222.52710.7544-0.3660.7290.40490.88110.2105-0.12580.51130.3705-0.30370.8671-0.8059-0.5631-0.05290.55470.11210.14320.36120.03360.6187-9.192516.691325.5392
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 305:338)A305 - 338
2X-RAY DIFFRACTION2chain 'A' and (resid 339:395)A339 - 395
3X-RAY DIFFRACTION3chain 'A' and (resid 396:405)A396 - 405
4X-RAY DIFFRACTION4chain 'A' and (resid 406:420)A406 - 420
5X-RAY DIFFRACTION5chain 'A' and (resid 421:438)A421 - 438
6X-RAY DIFFRACTION6chain 'A' and (resid 439:496)A439 - 496
7X-RAY DIFFRACTION7chain 'A' and (resid 497:531)A497 - 531
8X-RAY DIFFRACTION8chain 'A' and (resid 532:548)A532 - 548
9X-RAY DIFFRACTION9chain 'B' and (resid 305:322)B305 - 322
10X-RAY DIFFRACTION10chain 'B' and (resid 323:338)B323 - 338
11X-RAY DIFFRACTION11chain 'B' and (resid 339:363)B339 - 363
12X-RAY DIFFRACTION12chain 'B' and (resid 364:394)B364 - 394
13X-RAY DIFFRACTION13chain 'B' and (resid 395:407)B395 - 407
14X-RAY DIFFRACTION14chain 'B' and (resid 408:420)B408 - 420
15X-RAY DIFFRACTION15chain 'B' and (resid 421:437)B421 - 437
16X-RAY DIFFRACTION16chain 'B' and (resid 438:455)B438 - 455
17X-RAY DIFFRACTION17chain 'B' and (resid 456:472)B456 - 472
18X-RAY DIFFRACTION18chain 'B' and (resid 473:496)B473 - 496
19X-RAY DIFFRACTION19chain 'B' and (resid 497:531)B497 - 531
20X-RAY DIFFRACTION20chain 'B' and (resid 532:548)B532 - 548
21X-RAY DIFFRACTION21chain 'C' and (resid 688:696)C688 - 696
22X-RAY DIFFRACTION22chain 'D' and (resid 686:696)D686 - 696

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