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

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Basic information

Entry
Database: PDB / ID: 5kcd
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with an N-methyl Substituted OBHS-N derivative
Components
  • Estrogen receptor
  • NCOA2Nuclear 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 / 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 / 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 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
Chem-OB2 / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsNwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Dharmarajan, V. / Goswami, D. / Kastrati, I. / Novick, S. / Nowak, J. / Zhou, H.B. / Boonmuen, N. ...Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Dharmarajan, V. / Goswami, D. / Kastrati, I. / Novick, S. / Nowak, J. / Zhou, H.B. / Boonmuen, N. / Zhao, Y. / Min, J. / Frasor, J. / Katzenellenbogen, B.S. / Griffin, P.R. / Katzenellenbogen, J.A. / Nettles, K.W.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Full antagonism of the estrogen receptor without a prototypical ligand side chain.
Authors: Srinivasan, S. / Nwachukwu, J.C. / Bruno, N.E. / Dharmarajan, V. / Goswami, D. / Kastrati, I. / Novick, S. / Nowak, J. / Cavett, V. / Zhou, H.B. / Boonmuen, N. / Zhao, Y. / Min, J. / Frasor, ...Authors: Srinivasan, S. / Nwachukwu, J.C. / Bruno, N.E. / Dharmarajan, V. / Goswami, D. / Kastrati, I. / Novick, S. / Nowak, J. / Cavett, V. / Zhou, H.B. / Boonmuen, N. / Zhao, Y. / Min, J. / Frasor, J. / Katzenellenbogen, B.S. / Griffin, P.R. / Katzenellenbogen, J.A. / Nettles, K.W.
History
DepositionJun 6, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionNov 16, 2016ID: 4ZUC
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Dec 28, 2016Group: Database references
Revision 1.3Feb 26, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.4Mar 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
B: Estrogen receptor
C: NCOA2
D: NCOA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8326
Polymers61,9334
Non-polymers8992
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-23 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.945, 83.463, 58.779
Angle α, β, γ (deg.)90.000, 109.380, 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 NCOA2 / Nuclear receptor coactivator 2


Mass: 1666.943 Da / Num. of mol.: 2 / Fragment: Nuclear receptor-interacting peptide / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596*PLUS
#3: Chemical ChemComp-OB2 / (1S,2R,4S)-5,6-bis(4-hydroxyphenyl)-N-methyl-N-phenyl-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonamide


Mass: 449.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H23NO5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.1 Å3/Da / Density % sol: 41.32 % / Mosaicity: 0.28 °
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 8, 2011
RadiationMonochromator: Side scattering bent cube i-beam single crystal asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 45634 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 27.62 Å2 / Rmerge(I) obs: 0.04 / Χ2: 1.684 / Net I/av σ(I): 43.44 / Net I/σ(I): 19 / Num. measured all: 174399
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.82-1.853.80.2991100
1.85-1.893.80.2621100
1.89-1.923.80.2431100
1.92-1.963.80.2021100
1.96-23.80.1561100
2-2.053.80.1311100
2.05-2.13.80.1141100
2.1-2.163.80.0991100
2.16-2.223.80.091100
2.22-2.293.80.089199.9
2.29-2.373.80.0711100
2.37-2.473.80.0651100
2.47-2.583.90.0571100
2.58-2.723.90.0511100
2.72-2.893.90.0451100
2.89-3.113.90.0411100
3.11-3.433.90.0381100
3.43-3.923.90.0331100
3.92-4.943.80.03199.9
4.94-503.70.025196.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1690refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→44.606 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.39
RfactorNum. reflection% reflection
Rfree0.2053 1938 4.38 %
Rwork0.1771 --
obs0.1783 44249 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.32 Å2 / Biso mean: 40.9956 Å2 / Biso min: 16.28 Å2
Refinement stepCycle: final / Resolution: 1.82→44.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3764 0 64 315 4143
Biso mean--30.65 45.5 -
Num. residues----476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074057
X-RAY DIFFRACTIONf_angle_d1.0035509
X-RAY DIFFRACTIONf_chiral_restr0.042643
X-RAY DIFFRACTIONf_plane_restr0.004688
X-RAY DIFFRACTIONf_dihedral_angle_d15.771542
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 (%)
1.82-1.86550.24921290.20942817294691
1.8655-1.91590.28481300.22972791292190
1.9159-1.97230.25031190.21472885300492
1.9723-2.0360.22741470.19262975312296
2.036-2.10870.23471360.19232990312697
2.1087-2.19320.2291330.18743086321998
2.1932-2.2930.21931330.19182986311996
2.293-2.41380.20321550.18383075323099
2.4138-2.56510.24491390.18713133327299
2.5651-2.76310.20821370.184830983235100
2.7631-3.04110.2141500.189931083258100
3.0411-3.4810.20431460.180831393285100
3.481-4.38510.15911380.146831283266100
4.3851-44.61930.19961460.16773100324697
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)
19.1957-3.3915-0.32874.7888-0.62952.07360.02980.85840.1356-0.44640.07430.1393-0.1196-0.1842-0.17110.3239-0.0247-0.02770.41270.03780.21039.767523.7651-5.1367
22.7265-0.4617-0.55653.99960.30512.14880.0170.126-0.043-0.19780.0335-0.15910.02160.0753-0.00930.1659-0.04240.00410.2125-0.00270.147421.115117.19573.0047
35.2583-1.8672-0.00213.6215-1.21792.26350.03420.1389-0.27110.06490.04530.28150.0973-0.085-0.19220.1504-0.0305-0.00040.20160.01940.12699.835414.93157.5853
44.08870.1787-1.0312.053-0.12171.5239-0.01610.02080.1130.03430.0358-0.0262-0.03320.0185-0.03510.1887-0.0165-0.01190.1919-0.00240.146511.198420.531510.1779
54.6102-3.17410.35993.6353-1.13795.2913-0.4513-1.1178-0.29370.54620.3554-0.1501-0.4443-0.3549-0.03160.42580.14650.14050.44140.09220.23460.6820.467537.4296
63.327-0.5091.134.1283-0.77324.769-0.3155-0.28470.16230.45760.1577-0.1424-0.44440.11780.09040.31980.0553-0.00020.206-0.02550.1599.346423.024232.9776
74.9476-0.63841.25812.6935-0.16754.0318-0.0892-0.0342-0.16660.19460.11390.32870.0672-0.1511-0.01470.1862-00.05170.14080.00170.17660.489619.298421.1903
85.74523.59570.88447.1399-3.73549.5758-0.1663-0.150.42910.7069-0.1107-1.3652-0.74691.5407-0.0060.66490.0443-0.13670.71950.03690.636722.543513.531335.6663
90.2497-0.1583-0.06810.23720.11380.0578-0.00860.47490.6377-0.4473-0.0811-0.3016-0.4740.0165-0.00320.3254-0.04310.08330.28870.07130.512924.85436.80591.7317
100.0105-0.0053-0.00160.0124-0.00490.0070.2379-0.3584-0.28470.1082-0.017-0.13680.3232-0.159900.85780.118-0.00720.31050.11410.33179.78732.450738.7574
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 305 through 331 )A305 - 331
2X-RAY DIFFRACTION2chain 'A' and (resid 332 through 420 )A332 - 420
3X-RAY DIFFRACTION3chain 'A' and (resid 421 through 473 )A421 - 473
4X-RAY DIFFRACTION4chain 'A' and (resid 474 through 548 )A474 - 548
5X-RAY DIFFRACTION5chain 'B' and (resid 305 through 338 )B305 - 338
6X-RAY DIFFRACTION6chain 'B' and (resid 339 through 437 )B339 - 437
7X-RAY DIFFRACTION7chain 'B' and (resid 438 through 528 )B438 - 528
8X-RAY DIFFRACTION8chain 'B' and (resid 529 through 548 )B529 - 548
9X-RAY DIFFRACTION9chain 'C' and (resid 687 through 696 )C687 - 696
10X-RAY DIFFRACTION10chain 'D' and (resid 688 through 696 )D688 - 696

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