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

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Basic information

Entry
Database: PDB / ID: 5tlt
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with octane-1,8-diyl bis(2,3-bis(4-hydroxyphenyl)pentanoate)
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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / antral ovarian follicle growth / regulation of branching involved in prostate gland morphogenesis / 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 / epithelial cell development / steroid hormone receptor signaling pathway ...regulation of epithelial cell apoptotic process / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / antral ovarian follicle growth / regulation of branching involved in prostate gland morphogenesis / 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 / epithelial cell development / steroid hormone receptor signaling pathway / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / locomotor rhythm / mammary gland branching involved in pregnancy / uterus development / negative regulation of smooth muscle cell apoptotic process / aryl hydrocarbon receptor binding / vagina development / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / 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 / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of DNA-binding transcription factor activity / positive regulation of DNA-binding transcription factor activity / Nuclear signaling by ERBB4 / cellular response to hormone stimulus / Recycling of bile acids and salts / RNA polymerase II preinitiation complex assembly / transcription regulator inhibitor activity / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / protein localization to chromatin / : / 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 / negative regulation of canonical NF-kappaB signal transduction / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / ESR-mediated signaling / negative regulation of miRNA transcription / TBP-class protein binding / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / nuclear receptor binding / transcription corepressor binding / transcription coregulator binding / negative regulation of smoothened signaling pathway / 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 / euchromatin / Transcriptional activation of mitochondrial biogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / response to estrogen / RNA polymerase II transcription regulator complex / transcription coactivator binding / male gonad development / nuclear receptor activity / positive regulation of fibroblast proliferation / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / : / response to estradiol / PIP3 activates AKT signaling / HATs acetylate histones / positive regulation of cytosolic calcium ion concentration / 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 / regulation of inflammatory response / fibroblast proliferation
Similarity search - Function
Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 ...Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / 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-7ED / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 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
DepositionOct 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 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: NUCLEAR RECEPTOR COACTIVATOR 2
D: NUCLEAR RECEPTOR COACTIVATOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1246
Polymers61,7594
Non-polymers1,3662
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-26 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.347, 81.445, 58.024
Angle α, β, γ (deg.)90.000, 109.800, 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


Mass: 1579.866 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-7ED / 8-{[2,3-bis(4-hydroxyphenyl)pentanoyl]oxy}octyl (2R,3S)-2,3-bis(4-hydroxyphenyl)pentanoate / octane-1,8-diyl bis(2,3-bis(4-hydroxyphenyl)pentanoate)


Mass: 682.842 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H50O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 37.13 % / Mosaicity: 0.545 °
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: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 36933 / % possible obs: 98.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 32.63 Å2 / Rmerge(I) obs: 0.086 / Χ2: 1.031 / Net I/av σ(I): 28.125 / Net I/σ(I): 5.9 / Num. measured all: 252352
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.9-1.936.90.778199.6
1.93-1.976.90.634199.6
1.97-2.016.90.569199.5
2.01-2.056.80.459199.3
2.05-2.096.60.412199.4
2.09-2.146.60.33198
2.14-2.196.10.283197.1
2.19-2.257.10.245199.5
2.25-2.327.10.21199.3
2.32-2.3970.186199.5
2.39-2.4870.17199.3
2.48-2.586.90.149199.7
2.58-2.76.80.134199.3
2.7-2.846.30.12195.6
2.84-3.027.20.107199.8
3.02-3.257.10.095199.5
3.25-3.5870.084199.6
3.58-4.096.40.076196.8
4.09-5.167.10.068199
5.16-506.80.049197.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.903→45.869 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.98
RfactorNum. reflection% reflection
Rfree0.2205 1913 5.42 %
Rwork0.1737 --
obs0.1762 35289 94.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.99 Å2 / Biso mean: 44.578 Å2 / Biso min: 16.02 Å2
Refinement stepCycle: final / Resolution: 1.903→45.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3847 0 52 306 4205
Biso mean--44.03 49.58 -
Num. residues----493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063987
X-RAY DIFFRACTIONf_angle_d0.7745399
X-RAY DIFFRACTIONf_chiral_restr0.048641
X-RAY DIFFRACTIONf_plane_restr0.005672
X-RAY DIFFRACTIONf_dihedral_angle_d14.5872418
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 (%)
1.9027-1.95030.37691250.25662092221783
1.9503-2.0030.35711250.22952206233187
2.003-2.0620.26591240.21492231235590
2.062-2.12850.24891320.19592322245491
2.1285-2.20460.25061320.18692264239691
2.2046-2.29290.22261250.18632420254596
2.2929-2.39720.23381510.18122462261397
2.3972-2.52360.22661350.17842452258798
2.5236-2.68170.23281400.17432475261598
2.6817-2.88870.24291430.17782435257896
2.8887-3.17940.21681420.17132494263699
3.1794-3.63930.22561440.16982524266899
3.6393-4.58440.17451480.14872465261397
4.5844-45.88260.20771470.17222534268198
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)
12.726-0.6548-1.44454.85570.94055.21460.28360.96271.3389-0.4087-0.4273-0.3738-0.5445-0.41580.16780.36130.1001-0.03360.47460.10840.55112.265835.5488-4.2853
28.3199-3.9184-0.72848.95360.21233.68810.32681.1449-1.1685-0.243-0.8877-0.33170.85640.03530.49230.48390.06880.08580.55-0.02770.434621.23989.5804-6.9823
39.2075-4.4187-0.43169.30461.14454.4057-0.14090.1224-0.1413-0.06610.0979-0.4810.16720.4870.03670.2143-0.02290.03180.2956-0.01980.228221.355818.949-0.9602
43.41621.1501-0.07257.48680.90074.30330.0149-0.04530.28360.0466-0.0546-0.2614-0.19910.04670.04240.15690.030.01970.21280.02060.22514.242727.33394.8185
52.94570.2018-1.28484.93330.8642.7982-0.47150.7565-0.7341-0.383-0.2730.35140.2596-0.6760.61210.4562-0.07270.07270.3634-0.17560.406710.67796.9974-3.1806
64.27683.5371-0.11322.9335-0.04810.8978-0.0931-0.4009-1.28790.74760.1662-0.96820.54150.461-0.08331.12230.15770.16440.35440.01730.715518.42090.70615.3698
79.2873-1.89852.36155.2406-1.09415.8667-0.18220.2284-1.36480.26190.05630.13210.79670.04010.08230.5599-0.03990.1570.185-0.01120.43237.28397.59536.79
83.68632.71681.6243.32471.40136.4159-0.0952-0.010.2143-0.0739-0.03510.348-0.2607-0.22720.1920.22780.05080.00940.2822-0.01350.29934.301124.42034.2783
95.56485.47261.4129.51012.16776.55750.1828-0.34780.3143-0.4104-0.41350.1465-0.561-0.32690.23780.21580.0944-0.00390.31860.01230.2978-3.541930.71393.5971
102.5332-0.98672.19532.315-0.58443.48280.1741-0.3016-0.34840.1486-0.115-0.01360.43980.0495-0.04930.36660.01350.02070.21530.0070.23837.787317.250811.4426
118.5932-4.7776-3.64567.66384.94256.2294-0.3437-0.42380.3690.74680.2954-0.60440.80810.290.12720.36920.05440.02610.41970.04270.416928.415820.40499.0627
122.0587-0.7275-0.26992.34530.54244.30540.0175-0.1413-0.16020.0871-0.02640.05280.2468-0.17770.01730.2297-0.00320.01930.22760.02050.19061.042917.338833.2017
134.18870.0027-3.07589.3461.08616.62650.3509-0.7876-0.00150.10270.0443-1.1145-0.95351.0447-0.58380.5156-0.1146-0.01140.4279-0.07160.377111.392232.43634.9829
142.4826-0.40310.97591.4518-0.53154.5469-0.0260.0346-0.0968-0.051-0.0101-0.03990.15290.02580.05320.2697-0.01460.05360.2355-0.03680.24052.487320.69222.0816
157.6902-0.3987-2.79922.2617-3.54868.696-0.249-0.39631.3572-0.4332-0.2483-1.0787-1.14251.10820.18120.4372-0.09160.04990.4312-0.00420.681226.587733.72411.9596
162.55180.59312.39678.5203-2.06183.06540.2905-0.7047-1.86020.05070.09670.02150.4706-0.5968-0.29370.61130.0109-0.03180.40720.15980.60182.16212.118235.3752
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 303 through 322 )A303 - 322
2X-RAY DIFFRACTION2chain 'A' and (resid 323 through 338 )A323 - 338
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 363 )A339 - 363
4X-RAY DIFFRACTION4chain 'A' and (resid 364 through 394 )A364 - 394
5X-RAY DIFFRACTION5chain 'A' and (resid 395 through 407 )A395 - 407
6X-RAY DIFFRACTION6chain 'A' and (resid 408 through 420 )A408 - 420
7X-RAY DIFFRACTION7chain 'A' and (resid 421 through 437 )A421 - 437
8X-RAY DIFFRACTION8chain 'A' and (resid 438 through 472 )A438 - 472
9X-RAY DIFFRACTION9chain 'A' and (resid 473 through 496 )A473 - 496
10X-RAY DIFFRACTION10chain 'A' and (resid 497 through 531 )A497 - 531
11X-RAY DIFFRACTION11chain 'A' and (resid 532 through 548 )A532 - 548
12X-RAY DIFFRACTION12chain 'B' and (resid 305 through 394 )B305 - 394
13X-RAY DIFFRACTION13chain 'B' and (resid 395 through 421 )B395 - 421
14X-RAY DIFFRACTION14chain 'B' and (resid 422 through 549 )B422 - 549
15X-RAY DIFFRACTION15chain 'C' and (resid 687 through 696 )C687 - 696
16X-RAY DIFFRACTION16chain 'D' and (resid 688 through 696 )D688 - 696

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