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- PDB-5dz3: Crystal Structure of the ER-alpha Ligand-binding Domain in Comple... -

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Basic information

Entry
Database: PDB / ID: 5dz3
TitleCrystal Structure of the ER-alpha Ligand-binding Domain in Complex with the Cyclofenil Derivative 4,4'-{[4-(fluoromethyl)cyclohexylidene]methanediyl}diphenol
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 / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / prostate epithelial cord elongation / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / prostate epithelial cord elongation / 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 proliferation involved in mammary gland duct elongation / epithelial cell development / vagina development / locomotor rhythm / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / androgen metabolic process / regulation of lipid 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 / 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 / Recycling of bile acids and salts / cellular response to hormone stimulus / 14-3-3 protein binding / protein localization to chromatin / estrogen receptor signaling pathway / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / steroid binding / nitric-oxide synthase regulator activity / Regulation of lipid metabolism by PPARalpha / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / regulation of cellular response to insulin stimulus / ESR-mediated signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / transcription corepressor binding / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / 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 / nuclear receptor binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / circadian regulation of gene expression / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / euchromatin / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / transcription coactivator binding / beta-catenin binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / Constitutive Signaling by Aberrant PI3K in Cancer / male gonad development / nuclear receptor activity / Regulation of RUNX2 expression and activity / positive regulation of fibroblast proliferation / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / HATs acetylate histones / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / regulation of inflammatory response / positive regulation of cytosolic calcium ion concentration / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / fibroblast proliferation / 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) / 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 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 / 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
Chem-5JX / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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
DepositionSep 25, 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)62,5586
Polymers61,9334
Non-polymers6252
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-27 kcal/mol
Surface area20170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.986, 80.804, 58.073
Angle α, β, γ (deg.)90.000, 109.960, 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 / 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: 1666.943 Da / Num. of mol.: 2 / Fragment: Nuclear receptor-interacting peptide / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-5JX / 4,4'-{[4-(fluoromethyl)cyclohexylidene]methanediyl}diphenol


Mass: 312.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H21FO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 1.93 Å3/Da / Density % sol: 36.2 %
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: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 25367 / % possible obs: 99.1 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.04 / Rrim(I) all: 0.104 / Χ2: 0.908 / Net I/av σ(I): 20.294 / Net I/σ(I): 5.2 / Num. measured all: 169372
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.195.70.53711610.8570.2410.5910.48694
2.19-2.236.50.46112620.9110.1940.5010.47198.1
2.23-2.276.80.42912600.9170.1770.4650.47799.9
2.27-2.326.70.3713070.9350.1530.4010.513100
2.32-2.376.90.33812440.9520.1390.3650.529100
2.37-2.426.80.29412750.9580.1210.3180.51999.8
2.42-2.486.80.26612820.9590.110.2890.553100
2.48-2.556.80.23912680.9640.0990.260.602100
2.55-2.626.80.20912780.9740.0870.2270.63799.8
2.62-2.716.60.18212800.9790.0760.1970.68399.5
2.71-2.8160.16612240.9780.0720.1810.74697
2.81-2.926.70.14512570.9860.060.1570.8798.7
2.92-3.057.10.12613040.990.0510.1360.95799.8
3.05-3.217.10.11612720.9910.0470.1251.08299.9
3.21-3.416.90.09912660.9920.0410.1071.21899.9
3.41-3.686.80.08912740.9930.0370.0961.45999.7
3.68-4.056.20.07612750.9950.0330.0831.59898.9
4.05-4.636.70.07212650.9950.030.0781.70298.4
4.63-5.8370.06713020.9960.0270.0731.39399.8
5.83-506.60.06113110.9980.0250.0661.54299.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B1V

2b1v


Resolution: 2.15→45.762 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 1942 7.97 %
Rwork0.2017 22413 -
obs0.2043 24355 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.67 Å2 / Biso mean: 44.5204 Å2 / Biso min: 18.13 Å2
Refinement stepCycle: final / Resolution: 2.15→45.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3792 0 46 150 3988
Biso mean--35.01 42.49 -
Num. residues----489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023921
X-RAY DIFFRACTIONf_angle_d0.5425311
X-RAY DIFFRACTIONf_chiral_restr0.02636
X-RAY DIFFRACTIONf_plane_restr0.002656
X-RAY DIFFRACTIONf_dihedral_angle_d12.4191432
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1483-2.20210.2571110.24141340145180
2.2021-2.26160.27091360.2321500163690
2.2616-2.32810.25881280.2321552168093
2.3281-2.40330.2591370.2341574171193
2.4033-2.48920.28621440.22051597174196
2.4892-2.58880.2251390.22871617175696
2.5888-2.70660.23461420.2161622176496
2.7066-2.84930.26981370.22511561169894
2.8493-3.02780.23631490.20651642179198
3.0278-3.26150.27951380.20761659179798
3.2615-3.58960.23671510.2011681183299
3.5896-4.10880.18931380.17281664180298
4.1088-5.17550.2061500.17481680183099
5.1755-45.77280.23751420.20371724186699
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)
14.2262-0.17280.07943.63480.43521.9785-0.01210.23760.0947-0.12070.0188-0.15060.03120.05320.03050.2149-0.02650.00190.29960.02220.175615.2348.0027-0.6263
24.6476-0.9146-1.53374.20390.26021.7285-0.25860.0202-0.59280.24950.09430.08080.29650.02330.1070.3017-0.00810.02410.2582-0.01970.2529.2749-3.33233.8742
34.80870.0866-0.52582.13280.11061.74040.0571-0.40850.01810.1937-0.0406-0.05960.11440.16710.00980.2928-0.00690.01660.2268-0.02420.15139.14886.76818.3068
43.48360.45381.9522.18170.49684.45660.2196-0.3388-0.10610.0827-0.04280.08830.0896-0.53150.00150.314-0.01510.09590.3801-0.03880.3082-2.99166.280535.3903
52.0562-0.86650.61382.84740.70684.139-0.0026-0.2617-0.27820.1887-0.03850.15550.4509-0.0218-0.03670.3422-0.01510.05910.2441-0.00690.21373.2281-0.520931.5555
61.55310.7009-0.1774.4821-0.56385.0961-0.0047-0.18250.41060.14320.0977-0.6268-0.73790.55810.05560.459-0.0623-0.00370.3987-0.05690.383310.4217.265635.0398
76.1262-0.28741.53245.5058-0.07555.0645-0.3280.06780.28410.3896-0.0017-0.1877-0.95180.41850.15770.4082-0.06440.03560.280.01730.2328.359717.015324.498
81.84830.60151.01764.2602-0.2323.7152-0.02070.040.0552-0.0366-0.08520.1694-0.1566-0.43350.01220.2638-0.01020.0060.3394-0.02760.2203-4.80417.807923.7997
91.0241-1.5707-1.2212.3961.86171.43420.3276-0.46050.0869-0.8340.3686-0.31050.44160.1892-0.20810.9742-0.0456-0.08151.10910.330.52190.5027-10.90514.9521
102.6594-1.53320.38143.6191-0.69923.1019-0.1659-0.15530.1124-0.00090.03080.02320.2008-0.14670.06550.25570.0010.0880.2684-0.03880.16950.40455.37319.5247
113.3789-0.52020.48274.4365-0.14794.2395-0.1570.4967-0.13340.29930.2385-1.13341.26380.67610.14240.65080.1437-0.00340.38810.02370.742413.2119-7.013730.0597
124.54730.0026-0.21083.34563.41813.518-0.52420.42850.5855-0.7411-0.0522-0.5454-0.48840.0034-0.05820.4268-0.0397-0.04880.52270.00580.52626.051718.91831.5434
130.01370.01460.01110.0365-0.01620.02320.0159-0.4208-0.6328-0.01090.24780.25810.5897-0.3065-0.00040.696-0.0202-0.02370.45790.13420.59531.8702-13.123334.9033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 305 through 394 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 395 through 472 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 473 through 549 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 305 through 338 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 339 through 394 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 395 through 420 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 421 through 438 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 439 through 455 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 456 through 468 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 469 through 537 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 538 through 549 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 687 through 697 )C0
13X-RAY DIFFRACTION13chain 'D' and (resid 688 through 696 )D0

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