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

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Entry
Database: PDB / ID: 5tll
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with (E)-2-chloro-4'-hydroxy-4-((hydroxyiminio)methyl)-[1,1'-biphenyl]-3-olate
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 / cellular response to estrogen stimulus / mammary gland alveolus development / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / : / Nuclear signaling by ERBB4 / cellular response to hormone stimulus / RNA polymerase II preinitiation complex assembly / Recycling of bile acids and salts / protein localization to chromatin / negative regulation of canonical NF-kappaB signal transduction / estrogen receptor signaling pathway / positive regulation of adipose tissue development / : / steroid binding / 14-3-3 protein binding / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / 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 / stem cell differentiation / negative regulation of DNA-binding transcription factor activity / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / mRNA transcription by RNA polymerase II / circadian regulation of gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / euchromatin / transcription coactivator binding / 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 / male gonad development / positive regulation of fibroblast proliferation / 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-7EL / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.423 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 11, 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)62,2866
Polymers61,7594
Non-polymers5272
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-29 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.180, 82.380, 58.760
Angle α, β, γ (deg.)90.000, 110.940, 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-7EL / 2-chloro-4-[(E)-(hydroxyimino)methyl][1,1'-biphenyl]-3,4'-diol


Mass: 263.676 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H10ClNO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.06 Å3/Da / Density % sol: 40.18 % / Mosaicity: 1.273 °
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 26, 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.423→50 Å / Num. obs: 18716 / % possible obs: 98.1 % / Redundancy: 5.8 % / Biso Wilson estimate: 34.58 Å2 / Rmerge(I) obs: 0.131 / Net I/av σ(I): 16.5 / Net I/σ(I): 4.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.43-2.475.60.737198.3
2.47-2.525.80.684198.7
2.52-2.575.80.649199
2.57-2.625.80.552199
2.62-2.675.80.491198.8
2.67-2.745.50.419198.7
2.74-2.815.20.332191.3
2.81-2.885.50.353196.9
2.88-2.976.10.263199.3
2.97-3.066.10.226199.3
3.06-3.1760.199199.4
3.17-3.360.181199.2
3.3-3.455.90.148199.3
3.45-3.635.90.136199.3
3.63-3.865.70.118198.8
3.86-4.155.20.103192.3
4.15-4.576.10.108199.4
4.57-5.2360.104199.5
5.23-6.595.90.108198.5
6.59-505.50.094196.5

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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: 2.423→47.296 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.69
RfactorNum. reflection% reflection
Rfree0.2384 1612 10.04 %
Rwork0.1903 --
obs0.1952 16053 84.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.24 Å2 / Biso mean: 45.9891 Å2 / Biso min: 15.02 Å2
Refinement stepCycle: final / Resolution: 2.423→47.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3827 0 36 106 3969
Biso mean--44.77 37.49 -
Num. residues----487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023942
X-RAY DIFFRACTIONf_angle_d0.4725330
X-RAY DIFFRACTIONf_chiral_restr0.032632
X-RAY DIFFRACTIONf_plane_restr0.003662
X-RAY DIFFRACTIONf_dihedral_angle_d17.1161452
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4229-2.49420.17430.191141445729
2.4942-2.57470.2653870.220977786455
2.5747-2.66680.27811150.21941056117174
2.6668-2.77350.30471430.23231210135386
2.7735-2.89970.33231370.23371263140089
2.8997-3.05260.27811490.21851364151395
3.0526-3.24380.26871530.21881370152396
3.2438-3.49420.27231600.20141400156097
3.4942-3.84570.23411510.17891375152696
3.8457-4.40180.19381530.15661353150695
4.4018-5.54440.19311620.15851442160499
5.5444-47.30550.21941590.18881417157697
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)
14.58371.31740.59812.3849-0.21945.38980.08450.3332-0.4828-0.10510.0573-0.14480.18170.537-0.08860.2192-0.04290.03630.3288-0.06030.32611.2534.792919.8236
23.4010.43310.28553.9916-0.76786.3318-0.07890.2323-0.1467-0.0740.02370.05380.2149-0.14640.06550.19490.00590.04030.2177-0.01180.14553.8542.100522.2611
35.0008-0.8032-0.02164.40020.16123.5761-0.04960.10860.13620.60590.15210.3991-0.4587-0.2524-0.11270.35940.07550.07580.32190.04810.1652.16379.584829.8774
44.3210.60010.88443.17640.22634.469-0.03070.24730.08150.1261-0.0769-0.0189-0.06740.41110.12520.2038-0.0030.0560.22110.02980.14638.3655.64336.4469
55.47252.172-1.8086.13611.37512.0046-0.03440.4586-0.77540.1253-0.05570.46860.5919-1.98040.08840.4907-0.0611-0.04140.6547-0.09240.504-7.2427-7.207421.5498
64.79272.1803-1.13685.6965-0.37124.19510.3387-0.53250.46920.7597-0.4040.4583-0.34030.13050.01270.28310.0353-0.02420.3382-0.05470.1697-3.57565.892860.6798
75.02890.5263-1.07674.0242-1.41133.45150.0677-0.103-0.04410.2734-0.05990.3606-0.0449-0.20060.00970.1741-0.01850.02580.2045-0.02490.159-8.73582.999353.9356
85.62980.7965-0.70433.9157-0.28673.0082-0.03270.2723-0.60620.2147-0.05270.07620.42340.02420.10550.3049-0.00950.05760.2059-0.04380.1963-0.9544-2.28348.7728
96.19180.5507-0.98943.0857-0.53932.7156-0.0130.24790.16950.1416-0.00910.2445-0.039-0.1186-0.00950.282-0.0230.03530.2135-0.0240.1438-1.45355.893946.35
102.0021-4.62092.73227.96092.32244.2168-0.31261.128-1.39930.0160.06050.37950.44080.79620.2640.81090.0679-0.01040.4342-0.0520.40136.8646-14.286319.1983
116.62370.34163.4556.83113.09157.7279-0.06190.01051.3518-0.2387-0.37410.1592-0.6791-0.73280.44760.42740.07950.17350.3580.07860.6546-18.553216.522454.0813
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 305 through 338 )A305 - 338
2X-RAY DIFFRACTION2chain 'A' and (resid 339 through 411 )A339 - 411
3X-RAY DIFFRACTION3chain 'A' and (resid 412 through 470 )A412 - 470
4X-RAY DIFFRACTION4chain 'A' and (resid 471 through 531 )A471 - 531
5X-RAY DIFFRACTION5chain 'A' and (resid 532 through 548 )A532 - 548
6X-RAY DIFFRACTION6chain 'B' and (resid 305 through 338 )B305 - 338
7X-RAY DIFFRACTION7chain 'B' and (resid 339 through 411 )B339 - 411
8X-RAY DIFFRACTION8chain 'B' and (resid 412 through 470 )B412 - 470
9X-RAY DIFFRACTION9chain 'B' and (resid 471 through 548 )B471 - 548
10X-RAY DIFFRACTION10chain 'C' and (resid 688 through 696 )C688 - 696
11X-RAY DIFFRACTION11chain 'D' and (resid 688 through 696 )D688 - 696

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