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

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Basic information

Entry
Database: PDB / ID: 5kri
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with 16b-benzyl 17b-estradiol
Components
  • Estrogen receptor
  • NCOA2
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 / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / uterus development / mammary gland branching involved in pregnancy / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / steroid hormone receptor signaling pathway / regulation of lipid metabolic process / androgen metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / cellular response to estrogen stimulus / mammary gland alveolus development / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Mitochondrial unfolded protein response (UPRmt) / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / transcription regulator inhibitor activity / Nuclear signaling by ERBB4 / cellular response to hormone stimulus / Recycling of bile acids and salts / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / estrogen receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / positive regulation of adipose tissue development / 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 / positive regulation of nitric-oxide synthase activity / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / ESR-mediated signaling / positive regulation of DNA-binding transcription factor activity / transcription coregulator binding / response to progesterone / transcription corepressor binding / nuclear receptor binding / nuclear estrogen receptor binding / negative regulation of smoothened signaling pathway / negative regulation of DNA-binding transcription factor activity / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / transcription coactivator binding / euchromatin / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / response to estrogen / nuclear receptor activity / positive regulation of fibroblast proliferation / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / : / response to estradiol / PIP3 activates AKT signaling / HATs acetylate histones / ATPase binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / 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 / Nuclear receptor coactivators bHLH domain / : / 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-6WM / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.247 Å
AuthorsNwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Kojetin, D.J. / Elemento, O. / Katzenellenbogen, J.A. / Nettles, K.W.
CitationJournal: Cell Chem Biol / Year: 2017
Title: Systems Structural Biology Analysis of Ligand Effects on ER alpha Predicts Cellular Response to Environmental Estrogens and Anti-hormone Therapies.
Authors: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Wright, N.J. / Minutolo, F. / Rangarajan, E.S. / Izard, T. / Yao, X.Q. / Grant, B.J. / Kojetin, D.J. / Elemento, O. / ...Authors: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Wright, N.J. / Minutolo, F. / Rangarajan, E.S. / Izard, T. / Yao, X.Q. / Grant, B.J. / Kojetin, D.J. / Elemento, O. / Katzenellenbogen, J.A. / Nettles, K.W.
History
DepositionJul 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Mar 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)62,6586
Polymers61,9334
Non-polymers7252
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-29 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.857, 82.907, 58.585
Angle α, β, γ (deg.)90.00, 110.74, 90.00
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


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-6WM / (8~{R},9~{S},13~{S},14~{S},16~{R},17~{S})-13-methyl-16-(phenylmethyl)-6,7,8,9,11,12,14,15,16,17-decahydrocyclopenta[a]phenanthrene-3,17-diol


Mass: 362.505 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H30O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.02 Å3/Da / Density % sol: 39.03 % / Mosaicity: 0.415 °
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, 2012
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: 2.25→50 Å / Num. obs: 23169 / % possible obs: 98.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.05 / Net I/av σ(I): 33.841 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.25-2.296.80.422199.5
2.29-2.3370.31199.2
2.33-2.3870.278199.6
2.38-2.4270.218199.5
2.42-2.4870.195199.1
2.48-2.5370.199199.9
2.53-2.66.90.153199.2
2.6-2.676.90.147198.8
2.67-2.756.60.135198.3
2.75-2.8360.092196.2
2.83-2.947.20.082199.1
2.94-3.057.30.066199.5
3.05-3.197.20.061199.3
3.19-3.367.10.055199.1
3.36-3.5770.053199.6
3.57-3.856.80.044198.2
3.85-4.236.10.043195.9
4.23-4.857.30.035199.6
4.85-6.17.10.037199.2
6.1-506.80.034197.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.247→46.569 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2203 1930 8.65 %
Rwork0.2045 --
obs0.2059 22320 95.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.247→46.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3754 0 47 73 3874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043889
X-RAY DIFFRACTIONf_angle_d0.5565273
X-RAY DIFFRACTIONf_dihedral_angle_d13.3851409
X-RAY DIFFRACTIONf_chiral_restr0.044637
X-RAY DIFFRACTIONf_plane_restr0.003650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2468-2.3030.38521260.36721177X-RAY DIFFRACTION78
2.303-2.36530.25851250.26311422X-RAY DIFFRACTION93
2.3653-2.43490.27781350.23591431X-RAY DIFFRACTION95
2.4349-2.51350.25461320.23531458X-RAY DIFFRACTION95
2.5135-2.60330.26241500.24441430X-RAY DIFFRACTION95
2.6033-2.70750.26261190.2341436X-RAY DIFFRACTION94
2.7075-2.83070.2531410.241463X-RAY DIFFRACTION95
2.8307-2.97990.24881400.22721483X-RAY DIFFRACTION98
2.9799-3.16660.26941470.22571508X-RAY DIFFRACTION99
3.1666-3.4110.23061420.22371520X-RAY DIFFRACTION99
3.411-3.75420.21641390.20131509X-RAY DIFFRACTION99
3.7542-4.29710.21361450.16741481X-RAY DIFFRACTION96
4.2971-5.41260.17671460.16561537X-RAY DIFFRACTION100
5.4126-46.57910.17561430.1881535X-RAY DIFFRACTION97
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)
16.62781.5116-1.39292.8685-1.62256.2890.1211-0.37320.39330.535-0.18740.1111-0.570.46890.04750.4043-0.0447-0.04860.411-0.06940.2791-9.529-16.73075.7485
25.4433-0.212-1.61054.7809-1.65176.9175-0.10130.1088-0.2703-0.1245-0.03380.15850.6757-0.28940.12030.2743-0.05880.01420.2842-0.03180.2435-14.1395-23.9133-2.6131
35.4661-0.3575-3.05522.46931.36835.8810.1975-0.05110.67330.2795-0.2878-0.4224-1.00170.78180.13450.3957-0.207-0.03280.4143-0.00620.4212-0.3049-11.5326-4.7995
44.792-0.0472-3.49753.4282-0.52626.18080.02330.356-0.4559-0.4112-0.13050.49520.5015-0.71210.13420.4316-0.0454-0.03730.2876-0.00880.2847-13.1619-21.6447-10.8167
59.1141-1.84963.61112.8378-0.10972.5993-0.30220.5337-0.3706-0.3696-0.2099-1.2480.80722.21030.48510.43920.26820.15891.20720.2530.843516.9292-21.95-26.4823
65.6458-2.95560.42265.6187-0.51252.0969-0.19480.6609-0.0854-0.440.20831.1295-0.37-0.8661-0.09220.6893-0.0917-0.09790.7650.12630.5781-7.1738-14.0069-44.2466
72.0651-1.59221.3836.3436-0.86065.5635-0.51870.7201-0.8255-0.21270.28080.34860.554-0.39990.35720.6154-0.09210.10910.5501-0.01840.3909-4.7824-23.0297-37.6413
84.1747-1.0424-0.14346.27120.67264.6958-0.1497-0.3013-0.7571-0.4352-0.3744-0.42121.70550.42670.53770.73610.11860.18330.39090.10230.40560.495-27.1909-26.7997
99.30632.00360.15766.27445.6465.629-0.69011.38580.8743-0.59970.48950.5822-1.9529-0.29790.25260.69280.0487-0.06460.53570.12280.3485-5.6314-7.3996-36.0708
101.2589-1.69441.3084.3694-6.62232.0089-0.31690.3970.9177-0.29181.39541.20190.3694-2.4141-1.22810.66550.25830.04451.5020.18531.1933-19.6574-9.2855-33.2893
117.6648-0.210.26076.76680.84182.1529-0.2465-0.15630.504-0.19670.10721.0532-1.156-0.55630.15360.55260.04890.04520.47350.09010.3955-8.3472-8.0013-25.119
124.3472-1.938-0.64594.48971.64088.5389-0.0081-0.14370.036-0.0111-0.3909-0.4803-0.09771.1510.22420.30270.04650.03070.51130.14230.34545.779-16.0257-23.7402
132.6769-3.33422.90344.6011-5.18838.278-0.4548-0.7366-0.7860.88140.25580.66611.99090.35190.22351.08410.04930.30940.9632-0.01640.7605-1.0142-31.8477-15.6197
145.22531.4410.1625.11350.96857.62590.0579-0.4485-0.63050.5385-0.3625-1.2710.33341.37460.24910.3690.10110.02850.79680.13720.489412.517-20.1633-16.5053
157.54262.42230.98385.59150.85918.7624-0.51710.5481-0.0607-0.38840.17620.2226-0.4576-0.19920.36260.28250.02960.01950.29440.01610.2168-5.2551-16.272-19.7697
164.71180.2531.47957.52693.75826.54240.061-0.512-0.5620.5096-0.05750.21871.6715-1.3988-0.0830.9821-0.44340.13630.8282-0.17510.8421-12.958-31.3258-32.273
175.37971.9034-0.04674.3981-0.03050.00120.2836-0.13890.9392-0.2765-0.67110.1439-0.6504-1.1130.2260.48240.19750.16210.7140.07020.7786-25.26-6.5184-1.36
183.27520.66232.98138.82440.06215.30980.32730.4169-1.2363-0.6806-0.4043-0.66330.66560.07630.2891.05460.03420.22630.4679-0.14260.8041-0.3256-37.6447-35.1022
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 305 through 338 )
2X-RAY DIFFRACTION2chain 'A' and (resid 339 through 437 )
3X-RAY DIFFRACTION3chain 'A' and (resid 438 through 496 )
4X-RAY DIFFRACTION4chain 'A' and (resid 497 through 548 )
5X-RAY DIFFRACTION5chain 'B' and (resid 306 through 322 )
6X-RAY DIFFRACTION6chain 'B' and (resid 323 through 338 )
7X-RAY DIFFRACTION7chain 'B' and (resid 339 through 363 )
8X-RAY DIFFRACTION8chain 'B' and (resid 364 through 393 )
9X-RAY DIFFRACTION9chain 'B' and (resid 394 through 411 )
10X-RAY DIFFRACTION10chain 'B' and (resid 412 through 420 )
11X-RAY DIFFRACTION11chain 'B' and (resid 421 through 437 )
12X-RAY DIFFRACTION12chain 'B' and (resid 438 through 455 )
13X-RAY DIFFRACTION13chain 'B' and (resid 456 through 469 )
14X-RAY DIFFRACTION14chain 'B' and (resid 470 through 496 )
15X-RAY DIFFRACTION15chain 'B' and (resid 497 through 531 )
16X-RAY DIFFRACTION16chain 'B' and (resid 532 through 548 )
17X-RAY DIFFRACTION17chain 'C' and (resid 687 through 696 )
18X-RAY DIFFRACTION18chain 'D' and (resid 688 through 696 )

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