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

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Basic information

Entry
Database: PDB / ID: 5dvv
TitleCrystal Structure of the ER-alpha Ligand-binding Domain in Complex with a Triaryl-imine analog 4,4'-(phenylcarbonimidoyl)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 / 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 / TFIIB-class transcription factor binding / androgen metabolic process / 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 / Endogenous sterols / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Nuclear signaling by ERBB4 / 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 / RNA polymerase II preinitiation complex assembly / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / 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 / Regulation of lipid metabolism by PPARalpha / steroid binding / 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 / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / response to progesterone / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / nuclear estrogen receptor binding / transcription coregulator binding / stem cell differentiation / nuclear receptor binding / circadian regulation of gene expression / euchromatin / 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 / 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 / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / 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 / fibroblast proliferation / regulation of inflammatory response / 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
4,4'-(phenylcarbonimidoyl)diphenol / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.505 Å
AuthorsNwachukwu, J.C. / Wright, N.J. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Cavett, V. / Nowak, J. ...Nwachukwu, J.C. / Wright, N.J. / 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 21, 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)62,5126
Polymers61,9334
Non-polymers5792
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-34 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.830, 75.870, 57.840
Angle α, β, γ (deg.)90.000, 110.490, 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-5G6 / 4,4'-(phenylcarbonimidoyl)diphenol


Mass: 289.328 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H15NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 1.75 Å3/Da / Density % sol: 29.84 %
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: Jul 27, 2013
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: 2.5→50 Å / Num. obs: 14556 / % possible obs: 98.1 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.094 / Χ2: 0.997 / Net I/av σ(I): 23.424 / Net I/σ(I): 5.8 / Num. measured all: 96485
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.545.90.6156930.4497.5
2.54-2.596.20.5387330.48998.3
2.59-2.646.50.4797510.47198.6
2.64-2.696.30.4466960.49198.3
2.69-2.756.20.3837370.49998
2.75-2.825.80.3596870.52894.2
2.82-2.896.90.2677560.53799.3
2.89-2.967.10.287070.52499.7
2.96-3.0570.2017390.59699.5
3.05-3.157.20.1847420.60599.6
3.15-3.2670.1637270.62999
3.26-3.3970.1227410.75798.5
3.39-3.556.90.1187200.87998.8
3.55-3.736.80.0997331.10498.8
3.73-3.976.30.0887261.3597.2
3.97-4.276.10.096991.62695.8
4.27-4.77.10.0887561.70499.9
4.7-5.387.10.0827441.89999.2
5.38-6.786.70.0847371.89698.3
6.78-506.30.0597322.80993.8

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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: 2.505→49.488 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2576 1170 9.9 %
Rwork0.2197 10645 -
obs0.2236 11815 79.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.04 Å2 / Biso mean: 50.3972 Å2 / Biso min: 1.54 Å2
Refinement stepCycle: final / Resolution: 2.505→49.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 44 77 3299
Biso mean--21.22 39.29 -
Num. residues----431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023275
X-RAY DIFFRACTIONf_angle_d0.5464451
X-RAY DIFFRACTIONf_chiral_restr0.021554
X-RAY DIFFRACTIONf_plane_restr0.002547
X-RAY DIFFRACTIONf_dihedral_angle_d12.2591107
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5054-2.61950.3016510.240549154230
2.6195-2.75760.29961010.2539912101355
2.7576-2.93030.26871260.24841242136875
2.9303-3.15650.26681720.24121532170492
3.1565-3.47410.3051750.23071583175896
3.4741-3.97660.23331820.19661610179297
3.9766-5.00940.21121800.19231624180497
5.0094-49.49730.27351830.23081651183496
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)
16.2447-1.60610.03092.74140.52531.19740.20660.51160.2119-0.48391.2083-0.70970.03441.6665-0.02870.30170.04690.1651.387-0.15810.72420.94331.433125.5716
22.90311.1468-0.41624.3116-0.71748.5645-0.39040.33410.0185-0.33310.4223-0.04620.0763-0.1375-0.03080.33770.01790.08460.42630.0290.22651.01330.789415.1437
35.0107-0.2392-0.20241.9612-0.57818.49990.1980.10360.0673-0.5297-0.175-0.1405-0.2680.4503-0.05740.3414-0.03950.01920.28180.00170.14961.78182.793423.1533
43.93011.29690.54233.8773-1.30077.8383-0.54190.22161.8011-0.36810.55620.2356-2.4711-0.32480.1320.96860.04640.04820.35090.00730.4729-2.545415.02928.2601
52.97131.6203-0.52853.22360.36253.948-0.22680.22150.3366-0.1070.9378-0.5468-0.20641.8389-0.10880.2153-0.17560.11060.54560.00380.370610.16415.610629.5905
65.1652-0.36420.66513.08861.25725.47270.4028-1.030.19780.17080.0632-0.41780.92972.2683-0.14910.0609-0.01930.07251.0869-0.05610.430213.9306-1.080137.1509
77.67580.6711-1.09684.8794-0.4243.3019-0.01230.19690.52760.08180.29880.0344-0.53270.6554-0.19660.2572-0.05610.06670.44870.00210.20251.02817.073634.814
85.9905-3.4515-1.24145.6516-0.55923.27940.53350.7506-1.2459-0.99920.14951.36060.6685-0.9886-0.50830.6433-0.1468-0.13060.7132-0.22910.9424-9.4683-7.215720.7719
93.34140.04240.4822.3447-1.61971.26830.8147-1.00571.0895-0.13920.2675-1.4723-1.1491.0852-0.09470.4094-0.3328-0.16681.6455-0.5810.76715.645114.991458.9607
103.211-2.8821-1.77332.75050.36288.54770.1347-1.5915-0.1940.609-0.04150.1266-0.0343-0.1443-0.1140.3880.0448-0.08420.6930.1350.226-10.69170.210160.8988
116.38171.1304-1.37396.3227-0.97436.21450.6191-0.77550.49730.5182-0.49710.0252-0.5413-0.4143-0.17830.26840.01650.03430.24780.0110.2021-13.01057.244154.0077
126.2232-0.7137-1.92594.82050.11297.453-0.2592-0.4494-0.21810.14270.29540.27080.45860.2609-0.1070.1680.03-0.01130.2743-0.02480.1713-8.9199-0.567150.3893
137.2561-0.2188-1.07375.21431.05648.0693-0.5466-0.0991-1.279-0.10170.4566-0.7091.95290.58990.0740.8250.1150.07130.2733-0.0210.4837-2.5586-9.598745.542
145.1747-0.8071-1.41555.16941.39964.98220.3478-0.38440.1598-0.1030.3171-0.0039-0.60041.4731-0.19040.1758-0.0835-0.08950.7345-0.10540.18010.9596.664249.0719
153.7033-0.25390.47451.0857-0.17212.8523-0.1085-1.7773-0.37920.2649-0.7117-0.7907-0.28842.9185-0.418-0.0722-0.7761-0.48410.9849-0.87560.33459.968111.510450.4647
163.8039-0.4278-1.28843.41521.24615.3849-0.0015-0.5921-0.39090.0055-0.1410.03580.3632-0.03990.0410.3301-0.0794-0.04780.39680.02980.1888-5.9781-0.404242.1348
176.0587-0.2352-4.48638.05792.88315.3011-0.05320.03810.0727-0.5441-0.52820.4051-1.2618-2.02270.24030.25850.0491-0.07190.6544-0.03010.5054-20.94826.928844.2243
180.2080.2135-0.05340.39130.16920.2683-0.16210.3071-0.4461-0.13620.1093-0.10660.656-0.08650.08881.30290.13110.20640.5006-0.10750.58991.4451-14.079617.7476
190.7662-1.1690.16961.9675-1.14763.7662-0.835-0.28120.44670.3558-0.5273-0.2701-0.0327-0.43470.61820.79610.06210.0160.3807-0.02280.5666-19.953515.401151.9707
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 310 through 321 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 363 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 364 through 422 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 423 through 437 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 438 through 455 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 456 through 496 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 497 through 526 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 527 through 548 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 309 through 319 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 320 through 341 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 342 through 371 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 372 through 421 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 422 through 437 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 438 through 473 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 474 through 496 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 497 through 537 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 538 through 547 )B0
18X-RAY DIFFRACTION18chain 'C' and (resid 689 through 693 )C0
19X-RAY DIFFRACTION19chain 'D' and (resid 688 through 694 )D0

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