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

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Basic information

Entry
Database: PDB / ID: 5dxm
TitleCrystal Structure of the ER-alpha Ligand-binding Domain in Complex with the Cyclofenil Derivative 3-[(E)-(1s,5s)-bicyclo[3.3.1]non-9-ylidene(4-hydroxyphenyl)methyl]phenol
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-5J0 / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 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 23, 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)62,5746
Polymers61,9334
Non-polymers6412
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-30 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.506, 82.034, 58.843
Angle α, β, γ (deg.)90.000, 111.060, 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-5J0 / 3-[(E)-(1s,5s)-bicyclo[3.3.1]non-9-ylidene(4-hydroxyphenyl)methyl]phenol


Mass: 320.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H24O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.12 %
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: Nov 22, 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: 2.37→50 Å / Num. obs: 19078 / % possible obs: 96.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.031 / Rrim(I) all: 0.082 / Χ2: 0.714 / Net I/av σ(I): 22.545 / Net I/σ(I): 6.3 / Num. measured all: 128048
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.37-2.416.70.6219370.9080.2580.6740.4596.4
2.41-2.456.70.4889340.9350.2020.530.44795.4
2.45-2.56.50.4129690.9460.1710.4470.46199.4
2.5-2.556.60.3769610.9460.1570.4080.47696.5
2.55-2.616.40.3249590.970.1370.3520.51298.2
2.61-2.676.50.2689730.9760.1120.2910.51797.1
2.67-2.746.30.2379370.9790.1020.2590.5396.2
2.74-2.816.10.1928620.9840.0840.2110.54286.7
2.81-2.896.60.1819160.9860.0750.1970.55694.2
2.89-2.996.90.1429680.9930.0580.1530.56598
2.99-3.096.80.1249690.9950.0510.1340.62498.7
3.09-3.226.90.1099860.9940.0440.1180.63598.8
3.22-3.3670.0959710.9960.0390.1020.6798.9
3.36-3.546.90.0799560.9930.0330.0860.77798.3
3.54-3.766.80.0719800.9960.0290.0770.8998.4
3.76-4.056.50.0649220.9960.0270.071.06693.4
4.05-4.4670.0639410.9960.0250.0681.1493.9
4.46-5.17.10.0629820.9970.0250.0671.21398.6
5.1-6.436.90.069820.9970.0240.0650.99698.3
6.43-506.90.0429730.9990.0170.0451.05794.5

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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: 2.37→46.583 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2321 1827 9.99 %
Rwork0.1941 16466 -
obs0.1978 18293 92.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.63 Å2 / Biso mean: 60.9708 Å2 / Biso min: 18.28 Å2
Refinement stepCycle: final / Resolution: 2.37→46.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3785 0 48 77 3910
Biso mean--42.48 45.18 -
Num. residues----489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023929
X-RAY DIFFRACTIONf_angle_d0.5325330
X-RAY DIFFRACTIONf_chiral_restr0.022637
X-RAY DIFFRACTIONf_plane_restr0.003660
X-RAY DIFFRACTIONf_dihedral_angle_d12.7871423
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 (%)
2.3661-2.430.29141230.24841098122181
2.43-2.50150.28511320.24391198133088
2.5015-2.58230.29191360.24281229136589
2.5823-2.67460.26151310.23611241137290
2.6746-2.78160.31711180.25481206132489
2.7816-2.90820.28091440.24191208135288
2.9082-3.06150.25351400.22871339147996
3.0615-3.25330.26491540.22431310146497
3.2533-3.50440.2641500.20891312146298
3.5044-3.85690.24181520.191356150898
3.8569-4.41460.19911380.15331262140092
4.4146-5.56050.18171580.16511355151399
5.5605-46.5920.20281510.16881352150395
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)
13.7726-4.3767-1.51157.14561.21112.67230.61590.60370.6112-0.7886-0.7520.0516-0.7634-1.4166-0.14620.73470.4745-0.00260.84710.11160.58740.505518.0602-5.2151
21.48460.9965-0.69255.499-0.37663.23670.31240.4282-0.3203-0.5885-0.8345-0.66310.44050.45710.41240.52170.14890.01540.57010.08960.480721.0233-5.9702-6.4351
34.0047-0.5458-1.7064.21380.71946.4212-0.00130.23590.1306-0.0114-0.0388-0.14140.0954-0.09750.05580.22550.02310.00180.31570.01680.258715.68933.77441.0054
42.58091.0458-1.4111.2028-2.1916.05370.2842-0.3409-0.236-1.27550.2067-0.64531.7866-0.03770.16221.41840.20760.19910.58830.0250.963618.9812-15.35658.1406
57.2007-4.11360.81595.9385-0.61648.28950.07720.2139-0.8230.1779-0.31490.30351.5621-0.8045-0.04880.7163-0.11520.17480.3683-0.00450.55826.6522-7.73857.2603
65.9559-0.9588-1.69782.01360.02432.45640.44790.65190.2824-0.3638-0.40290.1254-0.5279-1.09570.05530.41140.16590.01760.68050.04080.38190.133211.8654.3912
75.6028-1.4088-2.55052.32580.83774.02080.103-0.123-0.19720.1668-0.0807-0.10060.34650.1424-0.07350.36360.028-0.04180.28510.02590.241512.81942.769210.7452
85.7399-0.8167-0.51941.85650.73596.5254-0.2991-0.244-0.18120.3347-0.02380.14990.4924-0.43010.30520.4781-0.01860.11480.4030.01590.3946-1.38262.481735.2955
93.7847-0.6008-1.81054.92330.55666.6134-0.0223-0.22190.13970.36090.0165-0.3807-0.25180.3051-0.06230.3137-0.0189-0.00580.30660.00320.20566.886310.476329.8923
102.51050.12780.96034.7725-2.26935.5822-0.08430.0632-0.0668-0.4885-0.10710.00660.4425-1.20520.08390.3705-0.07840.05780.6945-0.09740.3879-8.09593.013819.1127
113.265-0.72240.17312.6162-0.42527.1953-0.0006-0.0567-0.3680.0155-0.056-0.12460.36820.63040.02320.34880.02690.04010.3474-0.03650.36978.31043.700524.2886
126.0888-1.2334-1.06084.9630.69670.6854-0.04350.9938-0.37880.2786-0.7584-0.6702-0.73180.4605-0.03590.639-0.05630.24380.8265-0.10430.907825.13917.91830.5215
131.66710.19572.72170.5607-0.50535.7083-0.0582-0.8766-1.1587-0.30280.69720.26920.9648-0.7646-0.44211.0955-0.06750.17890.51810.25541.07990.3016-13.054236.6241
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 305 through 321 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 338 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 411 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 412 through 420 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 421 through 438 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 439 through 496 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 497 through 548 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 305 through 371 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 372 through 438 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 439 through 496 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 497 through 547 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 688 through 696 )C0
13X-RAY DIFFRACTION13chain 'D' and (resid 688 through 696 )D0

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