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

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Basic information

Entry
Database: PDB / ID: 5dzh
TitleCrystal Structure of the ER-alpha Ligand-binding Domain in Complex with the Cyclofenil Derivative 4,4'-{[4-(2-hydroxyethyl)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 / 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 / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis ...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 / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / epithelial cell development / mammary gland branching involved in pregnancy / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / uterus development / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / steroid hormone receptor signaling pathway / 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 / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / cellular response to hormone stimulus / Recycling of bile acids and salts / negative regulation of canonical NF-kappaB signal transduction / estrogen receptor signaling pathway / positive regulation of adipose tissue development / protein localization to chromatin / : / steroid binding / 14-3-3 protein binding / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / peroxisome proliferator activated receptor signaling pathway / TBP-class protein binding / regulation of cellular response to insulin stimulus / nitric-oxide synthase regulator activity / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / positive regulation of nitric-oxide synthase activity / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / ESR-mediated signaling / : / transcription coregulator binding / response to progesterone / nuclear receptor binding / transcription corepressor binding / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / stem cell differentiation / cellular response to estradiol stimulus / SUMOylation of intracellular receptors / circadian regulation of gene expression / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / euchromatin / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / response to estrogen / nuclear receptor activity / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of fibroblast proliferation / male gonad development / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / : / PIP3 activates AKT signaling / response to estradiol / HATs acetylate histones / 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 / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of inflammatory response
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 / 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-5KG / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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)62,5826
Polymers61,9334
Non-polymers6492
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-31 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.574, 81.954, 58.053
Angle α, β, γ (deg.)90.000, 111.000, 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-5KG / 4,4'-{[4-(2-hydroxyethyl)cyclohexylidene]methanediyl}diphenol


Mass: 324.413 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 1.96 Å3/Da / Density % sol: 37.32 %
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: 2.11→50 Å / Num. obs: 27404 / % possible obs: 98.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.109 / Χ2: 0.764 / Net I/av σ(I): 16.875 / Net I/σ(I): 4.5 / Num. measured all: 185587
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.11-2.1560.81713600.46798.6
2.15-2.195.80.72513150.47695.2
2.19-2.236.70.61513660.46799.5
2.23-2.2770.55913780.49599.9
2.27-2.3270.47413840.50499.7
2.32-2.3870.44113580.51399.5
2.38-2.446.90.35913650.52599.3
2.44-2.570.3313660.53699.4
2.5-2.586.90.29313840.57999.1
2.58-2.666.90.24113670.59798.6
2.66-2.756.60.20113530.64198.4
2.75-2.866.10.17813500.69197.8
2.86-2.997.20.14613740.773100
2.99-3.157.10.12713920.86799.9
3.15-3.357.10.11313770.976100
3.35-3.6170.0913901.09199.3
3.61-3.976.60.07413561.18197.9
3.97-4.546.60.06713621.23296.6
4.54-5.727.10.06613881.09799.9
5.72-506.70.06714191.44398.6

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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: 2.11→46.318 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 1891 7.25 %
Rwork0.1821 24181 -
obs0.1849 26072 93.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.59 Å2 / Biso mean: 47.0294 Å2 / Biso min: 12.11 Å2
Refinement stepCycle: final / Resolution: 2.11→46.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 0 48 174 4030
Biso mean--35.94 43.12 -
Num. residues----491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023942
X-RAY DIFFRACTIONf_angle_d0.6095339
X-RAY DIFFRACTIONf_chiral_restr0.023637
X-RAY DIFFRACTIONf_plane_restr0.003661
X-RAY DIFFRACTIONf_dihedral_angle_d13.5561440
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 (%)
2.1024-2.1550.25061130.23361419153278
2.155-2.21330.24491190.22861553167284
2.2133-2.27840.25611280.22681659178790
2.2784-2.35190.2731290.221695182492
2.3519-2.4360.29031450.20711703184893
2.436-2.53350.20421200.20691748186894
2.5335-2.64880.25961360.2141747188395
2.6488-2.78850.24981300.20771761189195
2.7885-2.96310.2121490.2051769191897
2.9631-3.19190.24321440.19371821196598
3.1919-3.5130.22551460.18061814196099
3.513-4.02110.19541410.15461812195397
4.0211-5.06510.18721420.14441812195498
5.0651-46.32960.20491490.17091868201799
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)
14.39271.221-0.76836.951-0.86842.98270.0680.9911.379-0.4795-0.33220.4-0.888-0.32310.10680.64630.244-0.05310.64070.1510.54891.475719.19-4.9102
22.43841.01040.20791.7494-2.76046.8480.03170.9817-0.6678-0.5063-0.7833-0.3221.32510.64320.47410.5910.13460.13190.42380.03390.356520.937-5.1845-6.7415
35.5047-1.5147-2.47195.34891.40654.44780.1590.2179-0.1323-0.02420.03530.0936-0.06920.2666-0.11910.1741-0.0346-0.01520.2257-0.00740.187521.17213.3794-0.8728
44.19720.0568-1.07334.68690.77944.4040.26490.02950.6684-0.1277-0.1383-0.1276-0.41790.0419-0.19960.1920.03310.03520.23340.02530.254614.032211.76654.7476
53.59892.1798-2.34153.4687-0.91874.0152-0.59850.5212-1.3314-0.3544-0.63370.35071.4102-0.70830.09420.4654-0.10440.1130.3748-0.18890.413711.8062-9.5576-2.817
60.9562-1.81580.63726.4442-0.54054.17980.3517-0.1078-0.2398-0.1510.2655-0.44530.86730.83950.0491.19730.15220.18850.54140.14780.859918.8759-13.96568.7636
72.0813-0.78361.22257.75720.42976.4113-0.1822-0.1698-0.81440.3322-0.02890.03860.5429-0.40160.15570.4266-0.08970.12180.28540.00070.37345.9126-7.77536.3648
87.4946-0.0507-0.67557.68550.70564.46870.11690.14080.47380.092-0.09610.0986-0.3316-0.34770.02050.26140.08720.0870.27420.00740.18864.45119.11094.6328
96.77050.9919-0.75836.26730.40194.06920.16560.31360.7629-0.7577-0.42450.3071-0.6091-0.44720.18830.37980.17670.00420.4460.03880.3352-3.987714.88063.1149
102.4281-0.36310.12393.578-0.16892.09490.01180.1371-0.39720.1017-0.10470.08150.0698-0.20150.06490.29780.00560.02390.2492-0.01810.18193.05272.471210.9842
115.6225-1.7563-2.30362.59871.01683.81250.8497-1.671-0.23350.56520.3219-0.9332-0.00810.5251-0.32510.490.0841-0.06141.03540.03160.73929.509-2.250513.7292
120.3791-0.53020.06213.1947-3.78615.6230.1776-0.9748-0.2990.60380.2212-0.4365-0.03470.8885-0.29580.3709-0.017-0.0430.53490.07480.50127.43095.95899.3701
138.10951.78434.14792.7150.90778.38130.2734-0.5923-0.70220.062-0.01180.1520.1364-1.2925-0.18580.27370.05770.04640.44810.03130.3508-9.17594.041131.786
140.7292-0.31542.43620.5267-0.69499.8624-0.123-1.25340.00240.36950.3014-1.36660.08212.277-0.29380.5327-0.0879-0.04471.1138-0.19641.052218.059513.451245.952
152.4314-0.5599-0.88813.42890.59734.5271-0.1408-0.15-0.13710.03530.0240.17520.1984-0.06540.06540.2231-0.00490.03080.22150.02580.19312.49342.34131.7212
164.95090.9875-2.56514.0242-3.52395.77530.6459-0.7898-0.05060.7192-0.3379-1.5094-2.41571.8296-1.05120.7217-0.18360.06640.7299-0.10130.552112.805617.657336.8393
173.54941.91011.24013.76010.96546.2134-0.03740.05120.2025-0.2079-0.0188-0.0961-0.9165-0.12230.04050.32610.00150.03850.2530.0140.2232.036612.229324.3321
188.20273.22341.24772.77893.78467.6869-0.83410.3553-1.1369-1.64180.20760.06451.10150.4651.13180.9519-0.07020.01250.7808-0.01610.57380.3272-10.851315.4117
194.5502-1.34710.72582.456-1.16934.2774-0.079-0.09950.0529-0.05630.00590.1135-0.0362-0.490.09860.2434-0.02070.0430.1979-0.02750.1631-1.82187.057917.9223
207.73941.8177-5.20255.3841-1.36259.0831-0.8198-0.4329-0.6752-0.56870.1794-1.27010.12111.41220.71190.54020.04380.07890.61780.20720.665215.2531-5.546132.496
217.29482.47483.36181.09191.38981.77440.1561-0.24571.30880.0261-0.1463-0.1653-0.99210.66130.08630.3803-0.08410.16270.44120.01340.807826.069518.06861.7026
224.53331.58350.15150.95690.8111.3901-0.5166-0.9635-2.33240.36390.468-0.0421.3863-0.49390.3250.7794-0.03360.05360.43420.28530.74471.0825-13.692635.5983
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 304 through 321 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 338 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 363 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 364 through 394 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 395 through 411 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 412 through 421 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 422 through 437 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 438 through 472 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 473 through 496 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 497 through 525 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 526 through 533 )A0
12X-RAY DIFFRACTION12chain 'A' and (resid 534 through 549 )A0
13X-RAY DIFFRACTION13chain 'B' and (resid 305 through 331 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 332 through 340 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 341 through 405 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 406 through 419 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 420 through 455 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 456 through 470 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 471 through 528 )B0
20X-RAY DIFFRACTION20chain 'B' and (resid 529 through 550 )B0
21X-RAY DIFFRACTION21chain 'C' and (resid 687 through 696 )C0
22X-RAY DIFFRACTION22chain 'D' and (resid 687 through 697 )D0

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