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- PDB-8vz1: Crystal Structure of the ER-alpha Ligand-binding Domain (L372S, L... -

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Basic information

Entry
Database: PDB / ID: 8vz1
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (L372S, L536S) in complex with k-409
ComponentsEstrogen receptor
KeywordsNUCLEAR PROTEIN / Estrogen Receptor
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / 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 ...regulation of epithelial cell apoptotic process / 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 / mammary gland branching involved in pregnancy / uterus development / negative regulation of smooth muscle cell apoptotic process / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of DNA-binding transcription factor activity / negative regulation of DNA-binding transcription factor activity / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / protein localization to chromatin / steroid binding / 14-3-3 protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / negative regulation of canonical NF-kappaB signal transduction / ESR-mediated signaling / negative regulation of miRNA transcription / TBP-class protein binding / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / transcription corepressor binding / transcription coregulator binding / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / 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 / positive regulation of cytosolic calcium ion concentration / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / DNA-binding transcription activator activity, RNA polymerase II-specific / fibroblast proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / calmodulin binding / Extra-nuclear estrogen signaling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type ...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 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
Similarity search - Domain/homology
: / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsMin, C.K. / Nwachukwu, J.C. / Hou, Y. / Russo, R.J. / Papa, A. / Min, J. / Peng, R. / Kim, S.H. / Ziegler, Y. / Rangarajan, E.S. ...Min, C.K. / Nwachukwu, J.C. / Hou, Y. / Russo, R.J. / Papa, A. / Min, J. / Peng, R. / Kim, S.H. / Ziegler, Y. / Rangarajan, E.S. / Izard, T. / Katzenellenbogen, B.S. / Katzenellenbogen, J.A. / Nettles, K.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Asymmetric allostery in estrogen receptor-alpha homodimers drives responses to the ensemble of estrogens in the hormonal milieu.
Authors: Min, C.K. / Nwachukwu, J.C. / Hou, Y. / Russo, R.J. / Papa, A. / Min, J. / Peng, R. / Kim, S.H. / Ziegler, Y. / Rangarajan, E.S. / Izard, T. / Katzenellenbogen, B.S. / Katzenellenbogen, J.A. / Nettles, K.W.
History
DepositionFeb 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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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: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8208
Polymers110,7984
Non-polymers2,0224
Water5,368298
1
A: Estrogen receptor
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4104
Polymers55,3992
Non-polymers1,0112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-12 kcal/mol
Surface area19290 Å2
MethodPISA
2
C: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4104
Polymers55,3992
Non-polymers1,0112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-12 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.529, 58.971, 93.745
Angle α, β, γ (deg.)86.51, 75.05, 63.02
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 27699.525 Da / Num. of mol.: 4 / Mutation: L372S, L536S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03372
#2: Chemical
ChemComp-A1AHS / 4,4'-[(1S,4S,5R)-5-(6-methoxy-3,4-dihydroquinoline-1(2H)-sulfonyl)-7-oxabicyclo[2.2.1]hept-2-ene-2,3-diyl]diphenol


Mass: 505.582 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H27NO6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.31 Å3/Da / Density % sol: 46.65 %
Crystal growTemperature: 298 K / Method: evaporation
Details: 20-25% PEG 3350, 200 mM MgCl2, 0.1 M Bis-Tris/Hepes/Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→37.477 Å / Num. obs: 59124 / % possible obs: 84.3 % / Redundancy: 7.7 % / CC1/2: 0.994 / Net I/σ(I): 6.3
Reflection shellResolution: 1.824→1.995 Å / Num. unique obs: 2957 / CC1/2: 0.641

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→35.39 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 35.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2745 2927 4.95 %
Rwork0.2248 --
obs0.2273 59112 66.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→35.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7141 0 141 298 7580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0177441
X-RAY DIFFRACTIONf_angle_d1.82510091
X-RAY DIFFRACTIONf_dihedral_angle_d21.2591075
X-RAY DIFFRACTIONf_chiral_restr0.1431201
X-RAY DIFFRACTIONf_plane_restr0.0111231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.850.388650.259368X-RAY DIFFRACTION2
1.85-1.880.3564120.2704210X-RAY DIFFRACTION5
1.88-1.910.2404200.278344X-RAY DIFFRACTION9
1.92-1.950.3774320.2759654X-RAY DIFFRACTION16
1.95-1.990.3258790.27211365X-RAY DIFFRACTION34
1.99-2.040.29571010.27182202X-RAY DIFFRACTION55
2.04-2.080.29891170.26122578X-RAY DIFFRACTION64
2.08-2.130.30531580.25642884X-RAY DIFFRACTION72
2.13-2.190.29561610.24843123X-RAY DIFFRACTION78
2.19-2.260.29371820.24863238X-RAY DIFFRACTION81
2.26-2.330.28431760.2423327X-RAY DIFFRACTION83
2.33-2.410.29721790.24273393X-RAY DIFFRACTION85
2.41-2.510.29491830.23163716X-RAY DIFFRACTION93
2.51-2.620.30071660.24043716X-RAY DIFFRACTION92
2.62-2.760.31482000.24443676X-RAY DIFFRACTION92
2.76-2.930.29021930.23523597X-RAY DIFFRACTION90
2.93-3.160.32291720.22423452X-RAY DIFFRACTION86
3.16-3.480.2442300.223738X-RAY DIFFRACTION94
3.48-3.980.25362010.19483682X-RAY DIFFRACTION92
3.98-5.010.24162000.18083504X-RAY DIFFRACTION88
5.01-35.390.25241600.23653718X-RAY DIFFRACTION92
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)
12.6421-0.3834-0.24211.4124-0.44421.6044-0.1027-0.08950.19980.012-0.5345-0.4639-0.0471.0177-0.21610.04140.04450.07970.87780.13880.48273.7523-27.314-9.537
25.1198-0.17550.25750.5414-0.07251.42370.1183-0.0391-0.29280.01240.02230.58880.3804-0.236-0.15280.4584-0.0020.09170.16340.01010.4151-19.9346-49.6152-7.6572
36.63775.49510.81664.9476-0.24492.49650.2335-0.01860.35780.4003-0.20110.25090.5073-0.0642-0.01460.33560.05350.05570.072-0.01890.2694-15.4603-41.151-1.2232
42.29380.87710.23354.37370.64184.69550.060.1471-0.1654-0.25910.05830.11870.158-0.0275-0.12010.10110.04020.00710.09230.01930.1503-17.4131-35.0765-6.6185
53.87490.30761.32544.2524-0.36863.97460.00380.0296-0.1035-0.3894-0.02350.1828-0.03810.01410.01260.1810.02240.01810.08770.03260.1391-15.7502-27.3446-11.3054
62.09-0.2568-0.72672.0917-0.2849.33410.1270.23170.3602-0.06550.0384-0.5263-0.97910.5755-0.14570.0097-0.02080.0540.3793-0.01250.2954-2.7357-18.3647-9.2965
72.4952-0.249-0.06582.6968-1.28753.7994-0.0026-0.0579-0.11740.13990.06320.2469-0.0157-0.0923-0.05880.1382-0.00580.04860.026-0.05440.1606-17.0943-27.1273-4.76
82222222.64851.2502-3.7647.4128-0.16613.41781.3104-1.7539-2.53741.1628-0.1248-0.39361.06940.30990.62331.4058-38.91566.6466
93.1363-0.0519-1.45812.30581.09453.6303-0.05010.34540.3024-0.82540.3090.332-0.6708-0.2701-0.10150.35080.08830.04880.16510.14350.2535-26.38540.3632-14.5925
102.88560.6335-0.22942.73071.48862.75250.0080.03290.0697-0.0867-0.06780.1945-0.3242-0.50580.06130.15630.0770.02010.09660.03720.1368-31.1484-6.6858-6.4988
112.3806-2.64731.68845.5321-3.3492.0369-0.472-1.5671-0.26221.53430.25340.2283-0.3816-0.59540.2260.6456-0.02970.04720.55880.05970.255-25.8466-5.636212.935
122.56940.13580.1632.39450.34973.7011-0.05510.0955-0.0089-0.07180.0368-0.0625-0.2865-0.11870.00120.19860.01120.03960.09080.01060.1228-22.2695-12.4905-10.7922
135.0564-2.2636-1.0243.83331.12532.49780.0081-0.6252-0.06830.0418-0.0861-0.725-0.03330.82780.0460.1731-0.01690.04150.52110.08160.3557-20.1664-22.9593-49.3972
147.8529-0.6678-0.09240.43910.50731.1111-0.34040.38420.57410.35270.11460.1364-0.3299-0.13340.15660.328-0.0365-0.01790.18650.0440.3052-42.9819-1.0599-52.4899
157.6655-6.18012.45085.5278-1.22852.7336-0.23630.1657-0.0714-0.00460.04370.0176-0.35280.02590.16180.1549-0.0480.02720.0612-0.00950.169-39.535-9.0392-58.7138
162.2624-0.1574-0.90323.14531.38394.8255-0.00670.06140.0614-0.19650.0235-0.08010.07190.43290.06150.1169-0.0320.06030.09730.0260.1931-35.0107-20.3115-58.7536
171.7276-0.8394-1.74515.12640.22834.8597-0.0577-0.40880.14270.5972-0.0734-0.0707-0.18540.38960.07150.2195-0.03580.08530.2389-0.03260.2328-44.7037-9.6942-42.3991
183.13990.80640.30195.2467-0.52836.60930.113-0.07060.22360.29290.26341.3779-0.1455-1.51910.29430.32710.02990.05050.359-0.02850.4451-53.1947-7.1105-48.4409
198.351-1.97433.05163.4842-0.78426.0861-0.2639-0.6070.24560.48880.07590.7430.0095-0.6898-0.12230.1645-0.03590.11060.2713-0.05530.3197-48.6867-18.6051-43.7761
202.7827-0.9077-0.49913.4019-0.89616.2421-0.02750.06760.0725-0.2474-0.09750.14770.40070.18450.11330.0756-0.03730.0170.07890.0040.2173-34.0596-26.0979-52.7473
210.95340.6521-0.08763.3926-0.47792.1580.10730.0085-0.0263-0.09360.0454-0.22630.61120.5298-0.24760.09970.02640.03320.27880.0080.2029-26.6432-31.872-50.8259
223.4671-0.86992.62212.7499-1.1544.7329-0.1779-0.08180.0647-0.02840.03050.1858-0.06560.01430.02790.1176-0.0230.03140.1309-0.02210.1865-42.1111-27.6253-47.6665
238.6825.1767-3.42674.8773-1.7355.41470.69680.39610.5478-0.3572-0.4894-0.0049-0.2153-0.2648-0.41450.3725-0.0212-0.02220.31370.09410.2045-36.5967-14.7417-69.4459
242-2.66052222-0.49324.5731-7.093-3.2803-5.0171-1.79211.579511.55315.56630.8474-0.2668-0.03790.84320.05360.9812-23.0076-12.4417-65.9097
255.26921.22273.22242.96061.63987.7370.1164-0.4231-0.23630.5342-0.03210.24090.3692-0.5461-0.08020.3108-0.06170.05280.10490.01610.2234-50.4575-50.4121-45.2714
264.26330.67222.26473.42052.50172.68-0.15120.07130.06580.21620.03610.4494-0.31630.2203-0.01620.2383-0.12170.06350.1920.05520.2584-58.9831-44.614-50.6723
273.80340.21110.17273.88231.1652.56710.00110.2766-0.0435-0.437-0.03750.1875-0.064-0.2225-0.05960.1389-0.09760.02170.12410.04170.1693-51.5824-42.8294-58.667
287.9507-3.36254.39862.1211-2.24576.60490.15641.06180.1521-0.8844-0.2881-0.09070.29890.45140.19550.2785-0.00130.01890.3-0.00160.2044-42.2958-40.0512-64.3024
296.4112-1.417-1.21354.4977-0.36623.6076-0.0169-0.28580.38390.25920.0489-0.05420.147-0.12230.14820.2274-0.0761-0.0030.1081-0.02470.1335-46.2445-38.9669-45.9487
306.425-1.4909-0.98086.50850.82475.89560.0424-0.20760.35020.69240.0139-0.38730.43720.03020.03870.2910.0081-0.0250.15080.05070.0988-40.2237-40.6756-38.1374
313.0649-3.08924.15583.9545-3.49297.32710.13360.1421-0.3374-0.34890.030.2640.1961-0.0177-0.1230.1928-0.05390.05540.0727-0.02090.1956-43.1058-34.7229-55.0265
322.15821.0628-3.54067.7107-5.80198.2090.1007-0.26310.3398-0.27890.60420.7070.8173-1.6066-0.38270.2168-0.10620.07510.7227-0.05270.5393-66.4816-36.6554-51.3413
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 305 through 322 )
2X-RAY DIFFRACTION2chain 'A' and (resid 323 through 338 )
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 363 )
4X-RAY DIFFRACTION4chain 'A' and (resid 364 through 421 )
5X-RAY DIFFRACTION5chain 'A' and (resid 422 through 465 )
6X-RAY DIFFRACTION6chain 'A' and (resid 466 through 496 )
7X-RAY DIFFRACTION7chain 'A' and (resid 497 through 546 )
8X-RAY DIFFRACTION8chain 'A' and (resid 547 through 547 )
9X-RAY DIFFRACTION9chain 'B' and (resid 305 through 341 )
10X-RAY DIFFRACTION10chain 'B' and (resid 342 through 407 )
11X-RAY DIFFRACTION11chain 'B' and (resid 408 through 421 )
12X-RAY DIFFRACTION12chain 'B' and (resid 422 through 546 )
13X-RAY DIFFRACTION13chain 'C' and (resid 306 through 321 )
14X-RAY DIFFRACTION14chain 'C' and (resid 322 through 338 )
15X-RAY DIFFRACTION15chain 'C' and (resid 339 through 363 )
16X-RAY DIFFRACTION16chain 'C' and (resid 364 through 395 )
17X-RAY DIFFRACTION17chain 'C' and (resid 396 through 405 )
18X-RAY DIFFRACTION18chain 'C' and (resid 406 through 421 )
19X-RAY DIFFRACTION19chain 'C' and (resid 422 through 437 )
20X-RAY DIFFRACTION20chain 'C' and (resid 438 through 465 )
21X-RAY DIFFRACTION21chain 'C' and (resid 466 through 496 )
22X-RAY DIFFRACTION22chain 'C' and (resid 497 through 525 )
23X-RAY DIFFRACTION23chain 'C' and (resid 526 through 546 )
24X-RAY DIFFRACTION24chain 'C' and (resid 547 through 547 )
25X-RAY DIFFRACTION25chain 'D' and (resid 305 through 341 )
26X-RAY DIFFRACTION26chain 'D' and (resid 342 through 371 )
27X-RAY DIFFRACTION27chain 'D' and (resid 372 through 420 )
28X-RAY DIFFRACTION28chain 'D' and (resid 421 through 437 )
29X-RAY DIFFRACTION29chain 'D' and (resid 438 through 469 )
30X-RAY DIFFRACTION30chain 'D' and (resid 470 through 496 )
31X-RAY DIFFRACTION31chain 'D' and (resid 497 through 528 )
32X-RAY DIFFRACTION32chain 'D' and (resid 529 through 546 )

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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