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- PDB-7ujm: Estrogen Receptor Alpha Ligand Binding Domain in Complex with a M... -

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Basic information

Entry
Database: PDB / ID: 7ujm
TitleEstrogen Receptor Alpha Ligand Binding Domain in Complex with a Methylated Lasofoxifene Derivative That Increases Receptor Resonance Time in the Nucleus of Breast Cancer Cells
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / Alpha helical bundle / hormone / estrogen receptor / breast cancer
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 / 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 ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / 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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / prostate epithelial cord elongation / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / steroid hormone receptor signaling pathway / mammary gland alveolus development / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / : / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / 14-3-3 protein binding / TBP-class protein binding / nitric-oxide synthase regulator activity / steroid binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / negative regulation of miRNA transcription / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / SUMOylation of intracellular receptors / euchromatin / negative regulation of DNA-binding transcription factor activity / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / response to estrogen / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / ATPase binding / regulation of inflammatory response / fibroblast proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / Extra-nuclear estrogen signaling / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) ...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 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
Similarity search - Domain/homology
Chem-RL4 / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHosfield, D.J. / Greene, G.L. / Fanning, S.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Elife / Year: 2022
Title: Stereospecific lasofoxifene derivatives reveal the interplay between estrogen receptor alpha stability and antagonistic activity in ESR1 mutant breast cancer cells.
Authors: Hosfield, D.J. / Weber, S. / Li, N.S. / Suavage, M. / Joiner, C.F. / Hancock, G.R. / Sullivan, E.A. / Ndukwe, E. / Han, R. / Cush, S. / Laine, M. / Mader, S.C. / Greene, G.L. / Fanning, S.W.
History
DepositionMar 31, 2022Deposition site: RCSB / Processing site: RCSB
SupersessionJun 15, 2022ID: 7KCD
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Estrogen receptor
A: Estrogen receptor
C: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,0468
Polymers120,3364
Non-polymers1,7104
Water12,322684
1
B: Estrogen receptor
A: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0234
Polymers60,1682
Non-polymers8552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-15 kcal/mol
Surface area20420 Å2
MethodPISA
2
C: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0234
Polymers60,1682
Non-polymers8552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-13 kcal/mol
Surface area20340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.467, 58.467, 275.346
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 30084.045 Da / Num. of mol.: 4 / Mutation: C381S, C417S, C530S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03372
#2: Chemical
ChemComp-RL4 / (5R,6S)-5-(4-{2-[(2R)-2-methylpyrrolidin-1-yl]ethoxy}phenyl)-6-phenyl-5,6,7,8-tetrahydronaphthalen-2-ol


Mass: 427.578 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H33NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 684 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 8,000, MgCl2, Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→44.33 Å / Num. obs: 75567 / % possible obs: 98.9 % / Redundancy: 3.9 % / Rpim(I) all: 0.033 / Net I/σ(I): 18.01
Reflection shellResolution: 1.8→1.85 Å / Num. unique obs: 3829 / CC1/2: 0.726

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UFX

5ufx


Resolution: 1.8→44.33 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2329 3829 5.11 %
Rwork0.1897 71141 -
obs0.192 74970 76.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.64 Å2 / Biso mean: 23.3838 Å2 / Biso min: 3.47 Å2
Refinement stepCycle: final / Resolution: 1.8→44.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7483 0 128 684 8295
Biso mean--19.62 30.27 -
Num. residues----951
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.820.2969860.25361297138338
1.82-1.850.2725820.26121433151543
1.85-1.870.29941060.23111589169547
1.87-1.90.33481160.24351922203857
1.9-1.930.24781240.22482233235765
1.93-1.960.31651130.23162425253869
1.96-1.990.28641350.22992602273778
1.99-2.020.26591400.22242670281077
2.02-2.060.29071570.23112752290981
2.06-2.10.25021410.21632728286979
2.1-2.140.24321600.21092743290380
2.14-2.190.27591410.19492772291381
2.19-2.240.25131570.19092724288178
2.24-2.30.20751330.19562743287682
2.3-2.360.27451490.18442757290679
2.36-2.430.2471480.19842695284379
2.43-2.510.23491370.18642755289281
2.51-2.60.25881600.18762732289280
2.6-2.70.25981490.19032714286380
2.7-2.820.25921510.19712771292280
2.82-2.970.23381250.18482799292481
2.97-3.160.22581320.19742868300083
3.16-3.40.23021650.18242998316387
3.4-3.740.18421720.16843213338594
3.74-4.290.20331730.15323385355899
4.29-5.390.18662020.163434233625100
5.4-44.330.20571750.19593398357399
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)
12.9069-0.91731.18611.2382-0.39612.20760.3057-0.6482-0.12410.421-0.2461-0.1950.18930.3716-0.0631-0.05020.7389-0.0589-0.68390.22010.34995.177-23.44825.969
21.18860.45120.08650.87520.35361.3569-0.2805-0.2837-0.30250.2813-0.12790.13890.8059-0.341-0.0469-0.0208-0.2115-0.02520.0198-0.03060.0786-16.146-16.55319.446
31.09240.75870.22970.7485-0.00912.3999-0.05320.05870.0727-0.1757-0.06670.00920.0268-0.32350.03560.0751-0.0317-0.0010.0632-0.01550.0838-11.745-10.17213.861
41.23180.05190.45440.6337-0.47161.5484-0.03860.0489-0.05310.0132-0.0079-0.0123-0.06760.08180.01560.08230.00250.00280.046-0.00890.0811-1.83-8.36516.45
51.3858-0.4332-1.39010.88571.03753.51350.8004-0.9169-0.30970.6025-0.6687-0.16950.17540.36120.0123-0.04510.2678-0.1384-0.09050.11320.15278.339-12.67127.43
63.4399-0.8073-0.47271.94920.3131.45480.1013-0.09910.1558-0.1512-0.07150.09630.04190.01530.04070.0783-0.02390.00010.0227-0.01990.0976-0.259-3.78615.15
71.6361-0.88511.35590.4427-0.71961.10910.0949-0.07550.10110.02880.13990.3228-0.2416-0.118-0.03080.16260.00840.03930.4296-0.03970.2873-23.464-1.43723.964
81.93350.5664-0.34384.1769-1.45342.5799-0.0896-0.0251-0.5090.3332-0.10020.07670.3322-0.1458-0.00520.2531-0.1172-0.10910.49730.0684-0.3909-16.421-16.20636.267
91.3-0.37110.06821.459-0.02771.167-0.1752-0.0852-0.0552-0.2260.04210.015-0.60850.2396-0.02890.1052-0.12890.00890.11280.01220.08579.59420.1918.087
100.66360.20440.08581.57950.02791.73080.0342-0.12110.02090.1671-0.11610.0355-0.0247-0.09110.03690.0754-0.0324-0.00370.0567-0.01140.07163.26913.08123.104
110.73420.2774-0.13891.47660.14971.4201-0.05760.021-0.0374-0.1212-0.0125-0.0626-0.01940.18470.03740.0238-0.0075-0.00060.0894-0.00040.09439.171.86415.695
122.05880.089-1.25860.0041-0.03230.79780.10240.06770.0986-0.47680.18770.5953-0.2417-0.4242-0.01430.50350.03710.0140.37060.06450.1929-4.13720.4787.32
131.2469-0.65760.17042.8725-0.75951.4284-0.03370.0518-0.1711-0.268-0.3490.1763-0.0292-0.90160.02240.0819-0.16840.06220.07660.0020.14216.093-18.48463.055
141.5119-0.71770.24520.81530.22251.6096-0.05060.12420.0212-0.0826-0.0526-0.0043-0.0644-0.0520.0275-0.0062-0.0125-0.01640.10160.00360.057814.398-12.58861.383
151.7144-0.55590.29120.8494-0.64071.5812-0.0891-0.1361-0.06110.15850.121-0.00420.0316-0.15460.01830.0719-0.01180.00630.07580.00390.087220.888-20.15169.391
161.31181.05770.51553.20511.33181.7013-0.1320.0252-0.2425-0.070.0877-0.12920.19670.3066-0.00740.15180.07350.06190.18950.01370.205650.716-24.3161.744
170.3304-0.13710.41920.0559-0.17760.51920.0073-0.14690.18850.22860.11050.0337-0.23210.11170.01060.6267-0.2273-0.15250.51540.08460.397757.4462.08878.578
181.10130.73280.84231.10220.45411.7504-0.10930.133-0.01610.01540.0601-0.0235-0.01380.2784-0.01280.04350.00150.00930.1542-0.0060.060748.741-13.11258.832
190.90870.26940.05250.91470.3561.7439-0.15180.06740.0269-0.00830.0213-0.0242-0.4522-0.00110.02640.0189-0.01390.00580.06620.00360.092341.457-13.95759.458
202.13080.1946-0.54510.34630.36331.81160.1396-0.38590.27130.297-0.26960.1902-0.03930.17210.00770.08220.0068-0.04430.26180.03880.12346.111-9.25879.055
210.98670.211-0.00071.00010.56441.7662-0.0308-0.0804-0.01370.0276-0.0214-0.039-0.0352-0.10820.00940.05370.02270.00080.08060.00430.097937.447-18.79966.933
220.56410.22980.18351.5004-1.47393.4125-0.42441.834-0.3847-0.31080.5797-0.13460.36230.08630.00560.12290.21410.059-0.4835-0.21830.169936.077-30.41855.364
231.40230.05890.14844.2394-0.65541.4523-0.085-0.00060.02160.00820.09680.05250.027-0.0080.00580.03720.0232-0.00560.0934-0.00060.081832.415-20.04968.005
240.8409-1.439-0.94562.38241.59561.0595-0.13390.34730.4945-0.31390.31670.0213-0.7106-0.0453-0.06010.3054-0.04650.02610.2740.01680.225643.668-2.46554.464
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 307:321 )A307 - 321
2X-RAY DIFFRACTION2( CHAIN A AND RESID 322:371 )A322 - 371
3X-RAY DIFFRACTION3( CHAIN A AND RESID 372:421 )A372 - 421
4X-RAY DIFFRACTION4( CHAIN A AND RESID 422:465 )A422 - 465
5X-RAY DIFFRACTION5( CHAIN A AND RESID 466:496 )A466 - 496
6X-RAY DIFFRACTION6( CHAIN A AND RESID 497:527 )A497 - 527
7X-RAY DIFFRACTION7( CHAIN A AND RESID 528:536 )A528 - 536
8X-RAY DIFFRACTION8( CHAIN A AND RESID 537:545 )A537 - 545
9X-RAY DIFFRACTION9( CHAIN B AND RESID 307:363 )B307 - 363
10X-RAY DIFFRACTION10( CHAIN B AND RESID 364:437 )B364 - 437
11X-RAY DIFFRACTION11( CHAIN B AND RESID 438:527 )B438 - 527
12X-RAY DIFFRACTION12( CHAIN B AND RESID 528:545 )B528 - 545
13X-RAY DIFFRACTION13( CHAIN C AND RESID 307:341 )C307 - 341
14X-RAY DIFFRACTION14( CHAIN C AND RESID 342:437 )C342 - 437
15X-RAY DIFFRACTION15( CHAIN C AND RESID 438:550 )C438 - 550
16X-RAY DIFFRACTION16( CHAIN D AND RESID 307:331 )D307 - 331
17X-RAY DIFFRACTION17( CHAIN D AND RESID 332:341 )D332 - 341
18X-RAY DIFFRACTION18( CHAIN D AND RESID 342:371 )D342 - 371
19X-RAY DIFFRACTION19( CHAIN D AND RESID 372:394 )D372 - 394
20X-RAY DIFFRACTION20( CHAIN D AND RESID 395:420 )D395 - 420
21X-RAY DIFFRACTION21( CHAIN D AND RESID 421:465 )D421 - 465
22X-RAY DIFFRACTION22( CHAIN D AND RESID 466:496 )D466 - 496
23X-RAY DIFFRACTION23( CHAIN D AND RESID 497:525 )D497 - 525
24X-RAY DIFFRACTION24( CHAIN D AND RESID 526:544 )D526 - 544

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