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- PDB-5tmz: Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) i... -

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Basic information

Entry
Database: PDB / ID: 5tmz
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with the estradiol derivative, (8S,9S,13S,14S,17S)-16-(3-methoxybenzyl)-13-methyl-7,8,9,11,12,13,14,15,16,17-decahydro-6H-cyclopenta[a]phenanthrene-3,17-diol
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION / Nuclear receptor / transcription factor / ligand binding / protein-ligand complex
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 ...regulation of epithelial cell apoptotic process / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / locomotor rhythm / mammary gland branching involved in pregnancy / uterus development / negative regulation of smooth muscle cell apoptotic process / aryl hydrocarbon receptor binding / vagina development / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / androgen metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Mitochondrial unfolded protein response (UPRmt) / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of DNA-binding transcription factor activity / negative regulation of DNA-binding transcription factor activity / Nuclear signaling by ERBB4 / cellular response to hormone stimulus / Recycling of bile acids and salts / RNA polymerase II preinitiation complex assembly / transcription regulator inhibitor activity / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / protein localization to chromatin / : / steroid binding / positive regulation of adipose tissue development / 14-3-3 protein binding / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / negative regulation of canonical NF-kappaB signal transduction / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / ESR-mediated signaling / negative regulation of miRNA transcription / TBP-class protein binding / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / nuclear receptor binding / transcription corepressor binding / transcription coregulator binding / negative regulation of smoothened signaling pathway / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / euchromatin / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Cytoprotection by HMOX1 / beta-catenin binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / response to estrogen / RNA polymerase II transcription regulator complex / transcription coactivator binding / male gonad development / nuclear receptor activity / positive regulation of fibroblast proliferation / 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 / : / response to estradiol / PIP3 activates AKT signaling / HATs acetylate histones / positive regulation of cytosolic calcium ion concentration / ATPase binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / DNA-binding transcription activator activity, RNA polymerase II-specific
Similarity search - Function
Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 ...Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / 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 / Nuclear receptor coactivators bHLH domain / PAS domain / : / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / 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
Chem-7FQ / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.207 Å
AuthorsNwachukwu, J.C. / Erumbi, R. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Izard, T. / Kojetin, D.J. / Elemento, O. / Katzenellenbogen, J.A. / Nettles, K.W.
CitationJournal: Cell Chem Biol / Year: 2017
Title: Systems Structural Biology Analysis of Ligand Effects on ER alpha Predicts Cellular Response to Environmental Estrogens and Anti-hormone Therapies.
Authors: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Wright, N.J. / Minutolo, F. / Rangarajan, E.S. / Izard, T. / Yao, X.Q. / Grant, B.J. / Kojetin, D.J. / Elemento, O. / ...Authors: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Wright, N.J. / Minutolo, F. / Rangarajan, E.S. / Izard, T. / Yao, X.Q. / Grant, B.J. / Kojetin, D.J. / Elemento, O. / Katzenellenbogen, J.A. / Nettles, K.W.
History
DepositionOct 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Estrogen receptor
C: Nuclear receptor coactivator 2
B: Estrogen receptor
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5446
Polymers61,7594
Non-polymers7852
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-29 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.630, 82.660, 58.460
Angle α, β, γ (deg.)90.000, 110.830, 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: 29299.535 Da / Num. of mol.: 2 / Fragment: ligand-binding domain (UNP residues 298-554) / 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 / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-7FQ / (9beta,13alpha,14beta,16alpha,17alpha)-16-[(4-methoxyphenyl)methyl]estra-1,3,5(10)-triene-3,17-diol


Mass: 392.530 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H32O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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 Å3/Da / Density % sol: 38.43 % / Mosaicity: 0.716 °
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: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2014
RadiationMonochromator: Side scattering bent cube i-beam single crystal asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 24431 / % possible obs: 99.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 25.54 Å2 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.049 / Rrim(I) all: 0.128 / Χ2: 1.263 / Net I/av σ(I): 21.667 / Net I/σ(I): 5.2 / Num. measured all: 162386
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.2-2.246.30.5590.915199.1
2.24-2.286.50.5410.905199.8
2.28-2.326.70.4890.941199.5
2.32-2.376.70.4380.9441100
2.37-2.426.70.3750.964199.8
2.42-2.486.80.3390.967199.8
2.48-2.546.70.3050.963199.8
2.54-2.616.70.2610.977199.8
2.61-2.696.60.2220.977199.6
2.69-2.776.10.1930.983198.7
2.77-2.876.20.1770.982198
2.87-2.9970.1530.9871100
2.99-3.1270.140.9871100
3.12-3.2970.1340.99199.9
3.29-3.496.80.1190.992199.7
3.49-3.766.70.1110.99199.8
3.76-4.1460.1040.988197.4
4.14-4.746.90.1050.989199.7
4.74-5.976.90.1050.991199.8
5.97-506.40.080.995198.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.207→46.443 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.7
RfactorNum. reflection% reflection
Rfree0.2423 1865 8.29 %
Rwork0.1882 --
obs0.1927 22490 91.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.47 Å2 / Biso mean: 40.3463 Å2 / Biso min: 1.63 Å2
Refinement stepCycle: final / Resolution: 2.207→46.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3949 0 42 148 4139
Biso mean--32.59 33.2 -
Num. residues----499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024128
X-RAY DIFFRACTIONf_angle_d0.4495597
X-RAY DIFFRACTIONf_chiral_restr0.033662
X-RAY DIFFRACTIONf_plane_restr0.003692
X-RAY DIFFRACTIONf_dihedral_angle_d13.2552497
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2067-2.26640.3181760.214881288847
2.2664-2.33310.30391180.21491416153483
2.3331-2.40840.28071430.21951561170491
2.4084-2.49450.26141530.2141622177594
2.4945-2.59430.29741550.22291617177294
2.5943-2.71240.26811300.21181646177696
2.7124-2.85540.27851580.21381618177694
2.8554-3.03420.26051500.20921700185098
3.0342-3.26840.24921510.20241740189199
3.2684-3.59730.23871620.19381697185999
3.5973-4.11750.2231420.16411708185098
4.1175-5.18650.21161640.154717341898100
5.1865-46.45350.19871630.16761754191799
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)
1-0.00090.00940.00680.08940.0340.0147-0.00040.070.1087-0.0050.00610.0982-0.0914-0.05020.05090.31560.5666-0.15230.36850.10390.31370.783119.1471-4.8547
20.39630.1029-0.13360.0869-0.01920.0481-0.01670.0941-0.1923-0.0036-0.1044-0.15790.1020.1014-0.05410.23170.1769-0.06920.2392-0.01920.163120.8017-6.0384-6.9686
30.05410.0215-0.08910.0495-0.04850.30040.1099-0.04460.08970.0006-0.0917-0.0576-0.04920.3243-0.00980.0875-0.0040.03680.0861-0.00570.147816.61077.90752.1508
40.0269-0.02110.02850.0864-0.04750.0737-0.07580.0346-0.0243-0.052-0.0723-0.00150.08020.0147-0.02750.2773-0.00640.0540.1231-0.06080.197311.2719-9.5378-2.9259
5-0.0007-0.0010.00030.00050.00150.0008-0.0351-0.025-0.00410.0116-0.003-0.04530.00870.0408-00.85710.16260.1890.41520.07950.65619.0599-14.73697.9369
60.2875-0.1689-0.15950.13240.18390.4953-0.11630.0623-0.01570.1641-0.11090.09250.3293-0.2087-0.3260.08440.07740.00590.0098-0.0120.17885.28292.16275.8227
70.3204-0.12770.02760.22340.14910.22270.09410.17270.1056-0.1124-0.28280.0134-0.0563-0.2982-0.39420.07140.1125-0.11750.23110.01590.07672.01677.18778.2651
80.05840.0309-0.05150.0484-0.02130.0621-0.0522-0.11810.0666-0.017-0.1629-0.1050.05420.0933-0.02580.11830.0198-0.01670.40330.050.331227.923.89948.8309
90.0540.0409-0.03150.0312-0.02450.01770.0197-0.0279-0.01390.0166-0.0486-0.0522-0.01650.0581-0.00970.1985-0.15550.09020.19980.04690.478325.360317.83151.1843
100.0236-0.02930.04820.0443-0.05750.11280.0851-0.0253-0.1165-0.03860.09280.09340.0856-0.05070.00910.2851-0.19750.04260.6588-0.15110.3163-17.69680.891825.1265
11-00.00270.0020.00430.00850.00450.0372-0.06070.0036-0.04220.049-0.1290.00060.1106-00.27830.0195-0.01980.3588-0.09080.22827.339710.034343.9029
120.29430.0337-0.31220.40920.08540.4384-0.3253-0.2146-0.28870.0173-0.07390.03420.61790.1157-0.49850.3272-0.00970.08140.0767-0.02370.15242.1346-0.871731.3723
130.03810.02010.01550.05960.02240.00910.0438-0.091-0.00140.07830.0393-0.0476-0.03180.09470.0250.3825-0.1237-0.05270.222-0.07750.13116.017317.349135.8422
140.00130.00070.0010.00030.00040.0003-0.00530.01710.0043-0.00530.0330.0095-0.01740.0214-00.6121-0.28330.03730.8561-0.33220.853219.512515.739633.6386
150.03270.00520.00920.01790.00580.0327-0.0189-0.0010.0191-0.06230.0115-0.0613-0.11850.1111-0.03860.3047-0.18250.03270.0999-0.09940.19178.977316.13625.4489
160.0077-0.00290.01920.005-0.02950.161-0.11370.0094-0.03440.0048-0.0315-0.0134-0.0828-0.2822-0.09230.08340.02890.00250.1816-0.09270.1421-5.75638.487523.4918
170.0043-0.0005-0.00020.00810.00070.0010.06190.00620.0005-0.01640.03320.01320.0240.0055-0.00010.5142-0.17750.16410.4289-0.03640.420.6111-9.780914.9334
180.13240.00440.07330.00960.04350.296-0.0496-0.0350.0667-0.0456-0.12780.06570.0135-0.3692-0.3688-0.24540.1496-0.1180.2162-0.00040.1363-1.92844.705618.193
190.0248-0.03330.0220.0583-0.03480.0211-0.0329-0.00330.0176-0.00840.02230.00440.01610.04580.01090.54330.40260.03490.37630.13430.381114.3028-5.892633.4481
200.0056-0.0104-0.00710.02410.0160.0237-0.0032-0.0081-0.0221-0.0229-0.0119-0.01040.0204-0.0241-0.01290.7366-0.13280.23550.11270.20270.3144-0.0565-13.454435.5691
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 304 through 321 )A304 - 321
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 338 )A322 - 338
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 394 )A339 - 394
4X-RAY DIFFRACTION4chain 'A' and (resid 395 through 411 )A395 - 411
5X-RAY DIFFRACTION5chain 'A' and (resid 412 through 421 )A412 - 421
6X-RAY DIFFRACTION6chain 'A' and (resid 422 through 471 )A422 - 471
7X-RAY DIFFRACTION7chain 'A' and (resid 472 through 529 )A472 - 529
8X-RAY DIFFRACTION8chain 'A' and (resid 531 through 548 )A531 - 548
9X-RAY DIFFRACTION9chain 'C' and (resid 687 through 696 )C687 - 696
10X-RAY DIFFRACTION10chain 'B' and (resid 304 through 321 )B304 - 321
11X-RAY DIFFRACTION11chain 'B' and (resid 322 through 338 )B322 - 338
12X-RAY DIFFRACTION12chain 'B' and (resid 339 through 394 )B339 - 394
13X-RAY DIFFRACTION13chain 'B' and (resid 395 through 411 )B395 - 411
14X-RAY DIFFRACTION14chain 'B' and (resid 412 through 420 )B412 - 420
15X-RAY DIFFRACTION15chain 'B' and (resid 421 through 437 )B421 - 437
16X-RAY DIFFRACTION16chain 'B' and (resid 438 through 455 )B438 - 455
17X-RAY DIFFRACTION17chain 'B' and (resid 456 through 465 )B456 - 465
18X-RAY DIFFRACTION18chain 'B' and (resid 466 through 531 )B466 - 531
19X-RAY DIFFRACTION19chain 'B' and (resid 532 through 548 )B532 - 548
20X-RAY DIFFRACTION20chain 'D' and (resid 688 through 697 )D688 - 697

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