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- PDB-6v87: Estrogen Receptor Alpha Ligand Binding Domain Y537S in Complex wi... -

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Basic information

Entry
Database: PDB / ID: 6v87
TitleEstrogen Receptor Alpha Ligand Binding Domain Y537S in Complex with 4-Hydroxytamoxifen
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / Estrogen Receptor / SERM / Activating Mutation / 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 / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. ...Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / Retinoid X Receptor / Retinoid X 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
4-HYDROXYTAMOXIFEN / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFanning, S.W. / Greene, G.L.
CitationJournal: To Be Published
Title: Estrogen Receptor Alpha
Authors: Fanning, S.W.
History
DepositionDec 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8434
Polymers60,0682
Non-polymers7752
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-5 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.201, 55.067, 97.479
Angle α, β, γ (deg.)90.0, 113.477, 90.0
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 30034.029 Da / Num. of mol.: 2 / 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) / References: UniProt: P03372
#2: Chemical ChemComp-OHT / 4-HYDROXYTAMOXIFEN


Mass: 387.514 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H29NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.14 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 3,350, MgCl2, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 19734 / % possible obs: 96.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 34.4257777406 Å2 / CC1/2: 0.912 / Rmerge(I) obs: 0.06 / Net I/σ(I): 2.83
Reflection shellResolution: 2.38→2.44 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.37 / Num. unique obs: 977 / CC1/2: 0.751 / Χ2: 0.704 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q50

4q50


Resolution: 2.4→39 Å / SU ML: 0.31476904227 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.0281451865
RfactorNum. reflection% reflection
Rfree0.2714 1798 10.027266151 %
Rwork0.2423 --
obs0.2452 17971 87.9379526326 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.5320194676 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3313 0 58 58 3429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005583269432743430
X-RAY DIFFRACTIONf_angle_d0.6938117550784635
X-RAY DIFFRACTIONf_chiral_restr0.0380982838817554
X-RAY DIFFRACTIONf_plane_restr0.0030654669648569
X-RAY DIFFRACTIONf_dihedral_angle_d13.80615379121232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.44980.2986760.2986670X-RAY DIFFRACTION48.0051480051
2.4498-2.52190.3411883132221000.289736988241849X-RAY DIFFRACTION61.4239482201
2.5219-2.60330.3286426314271300.2998358444621116X-RAY DIFFRACTION79.5149968092
2.6033-2.69630.3209573972561350.2907773803721284X-RAY DIFFRACTION91.0198845414
2.6963-2.80420.3361951398481530.2829232895471360X-RAY DIFFRACTION96.0025380711
2.8042-2.93180.2822510387021460.2786434043361364X-RAY DIFFRACTION97.861309138
2.9318-3.08630.3351166855411480.2676076555991387X-RAY DIFFRACTION97.8954081633
3.0863-3.27960.2856498250461640.2582857895431377X-RAY DIFFRACTION97.9656706929
3.2796-3.53270.2756957607221470.2523274302651373X-RAY DIFFRACTION97.6863753213
3.5327-3.88790.2700785476721400.2420871577361174X-RAY DIFFRACTION83.3756345178
3.8879-4.44980.2192758249091470.2032435465471395X-RAY DIFFRACTION97.1644612476
4.4498-5.60360.2271195152191540.2137133349941401X-RAY DIFFRACTION98.1691919192
5.6036-380.2609990384661620.2133998858521419X-RAY DIFFRACTION96.3436928702
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)
18.860968171352.735503664790.7574339662181.06335226121-0.5051553082145.33375395769-0.309883506258-0.5063384990813.09218139660.5957126874160.2021554510830.447321551073-1.40531797392-0.2381577536590.1224519639411.090997571770.2048423305280.1035726865540.349340408038-0.1103091702570.8245523402452.343937160728.6145035352626.3445714078
26.296120019536.71765961308-3.166203202912.11893588808-3.55641818513.91976984557-0.465106989672-0.02146288335650.182649448667-0.6049753728990.4350706400980.1875402879240.0462497783676-0.525347404045-0.03860781799070.3379158527370.0908114686039-0.03582680363040.324940196222-0.009884723151560.414067632167-14.7783217819-11.188065628621.6610461782
36.898232488693.866510913210.66658285943.61839255725-1.491205211062.838372847950.1603291384490.320311067036-0.250492031706-0.203355156317-0.206099950761-0.1544568203780.0399474669857-0.2992222642940.0310251093750.2224394079310.08941996729450.04218941713160.336145447951-0.07810557998750.294872509686-9.78899995489-9.8044003665115.4297978286
44.587633506032.64952398108-0.1681040674823.02188340959-2.069469628892.00880107101-0.2556728142360.1254766151231.25770786587-0.0587379036473-0.1508675347470.872650756467-1.581222066910.577821245030.3718579759480.569081759018-0.0191577934749-0.06062465655320.3219042088280.1091010832950.4309202736034.772093083694.9401604414512.075593538
56.079170827051.40160994872-1.178681322724.82823996837-2.510326153416.3780265323-0.4422973289190.05737646361060.02908542345870.03669686229660.144006666474-0.01385783918660.1923054875570.3695704831480.2532147623340.2318794349540.066426404071-0.009666075707070.225913287968-0.06061737658710.257380936050.321913369519-7.9902020795515.8142599291
66.995028619910.9650161123632.990256102082.628906135930.5103848982315.546028846930.156558264544-1.10834775678-0.3324511281130.7539992109470.02344356446880.7163103892850.57495163153-0.339745629201-0.147283566220.4000317213090.06240766910430.139819382140.7107261667770.3024492237750.584546911255-10.7959036685-16.790368072830.2337402877
78.615932647744.006874712463.838708845277.2859258454-2.225442405726.82841719057-0.823705142356-0.382956797362-2.77685354476-0.8487085686640.774018726065-1.196769750980.579842681551-0.7797561529740.1230830696850.653138080027-0.03117710071150.2100980413090.6339563959330.04475903719671.35000086562-9.974721709-28.100089268122.8199091515
85.081484102393.660757612432.4901626449710.15777409644.119191461078.999457191560.0829589227172-1.12033044843-1.053640307740.570712981929-0.308091112209-0.4133444646780.785775196689-0.2327698383070.2999453682250.3842733408510.1110963670770.09425551457950.515947913730.2129292842520.527380292237-0.476235012061-19.179743095830.0676363526
96.567263780610.9112457664821.577404928123.652082571150.4033208068433.67497990518-0.308513354781-0.6907271514890.9312093968150.2056297572670.225757071784-0.253103188491-1.11741466044-0.3877183925090.04966278974830.4475117468410.143151050324-0.05064572090450.296056475499-0.1418703180140.5163067195948.2137017391-0.19707071372927.344565977
107.581054542611.881860180822.992088625336.289440071123.158303744926.63121940246-0.051413966605-0.459966441122-0.2948773895620.1741357128710.1575087520050.06538805201810.06295379938560.229496332936-0.09419715967510.228574436850.1137591470410.04715198795110.315987202277-0.01645338363820.2688621347198.13691164594-13.262764583525.3453855786
112.50698815504-1.892292557041.138062784782.04789160223-7.449262483236.46336765949-0.183458048320.287251397557-0.0745747157292-2.361396978680.2921901167811.600160535290.932445928239-1.01586831405-0.171787733590.727249595743-0.0792605902856-0.1226984854980.917649840351-0.09487461573560.452633060059-5.6771404443-8.561451063274.75755018953
126.309538771311.00193988769-2.441946732146.180993850281.352650123688.38915562869-0.500452293786-1.437944321280.6618811705281.272873745750.454117012943-0.566332177470.6714072120250.6037574793520.0802846193870.4568529150.13156376748-0.1252869403970.503828536377-0.04000951139950.29201274958830.8059265724-15.934221801937.3745782701
135.32205956894-1.1005734406-0.05264177097676.554363554611.77293432383.536281939810.208488322546-0.106663499258-0.909489661294-0.192373737141-0.15922301590.2487400314960.4807789376050.314549563276-0.04977330730020.2763047555970.0991637178584-0.04257038387860.276833377165-0.01889690411770.3215116676625.1095306148-27.80065693621.7205312015
148.00060691927-2.75138029844-1.635457777366.701319270712.44200117126.029411384120.408597888721.835217060740.439092774919-1.09377104243-0.2181713792130.285924890717-0.4271876759240.32319887167-0.1458845187780.5525392457450.130882171890.05932136434280.6180457926270.1105734035160.3600941458426.5551484034-19.42346944155.1991665887
158.820817743285.638245741087.912316844569.529373587369.574176221582.39905444825-0.2471298677160.8371666426820.674318796641-1.43697868325-0.04215376380150.218788376402-1.292466393710.06280759908530.3433582575380.5134503030930.02555698049490.01799930954240.6165009309020.1423444941490.33729049155622.3628075768-11.470500367911.0598051247
165.385726490371.28914599767-0.7850327521217.883942518650.5807471749735.44309122626-0.130844579321-0.5241500049970.4761978851530.4974775369240.04529744866750.239139037777-0.300903556391-0.1866750054690.08661121292070.2626247083390.114998931734-0.07495131036680.305920467791-0.02385321762430.24382031455322.3136100774-12.340948519330.8354804961
175.629140631112.874391694643.583652074069.697452899355.606053352627.64362848284-0.10321539853-0.1575545068650.219101976547-0.481968788397-0.5404596454670.809581532534-0.407765160256-0.4908837251590.6066296208520.1983298370950.1101853981670.03273948731780.2634350262470.01725384561340.321385400416.000623821-12.729354798720.1065225681
182.23970992671.415047821170.007158143369723.95763553172.902126027282.74536612642-0.4201725471180.0990717917396-2.47310207645-0.0256031132966-0.4000087035370.1730100732662.63329097876-0.3851349775260.3642553393881.384344828520.1963937711590.523091955970.2599778015090.04298753462881.6514336447919.8037073305-37.658525216926.1141531248
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 309 through 321 )
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 338 )
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 363 )
4X-RAY DIFFRACTION4chain 'A' and (resid 364 through 371 )
5X-RAY DIFFRACTION5chain 'A' and (resid 372 through 394 )
6X-RAY DIFFRACTION6chain 'A' and (resid 395 through 412 )
7X-RAY DIFFRACTION7chain 'A' and (resid 413 through 420 )
8X-RAY DIFFRACTION8chain 'A' and (resid 421 through 437 )
9X-RAY DIFFRACTION9chain 'A' and (resid 438 through 496 )
10X-RAY DIFFRACTION10chain 'A' and (resid 497 through 526 )
11X-RAY DIFFRACTION11chain 'A' and (resid 527 through 545 )
12X-RAY DIFFRACTION12chain 'B' and (resid 307 through 321 )
13X-RAY DIFFRACTION13chain 'B' and (resid 322 through 394 )
14X-RAY DIFFRACTION14chain 'B' and (resid 395 through 423 )
15X-RAY DIFFRACTION15chain 'B' and (resid 424 through 437 )
16X-RAY DIFFRACTION16chain 'B' and (resid 438 through 496 )
17X-RAY DIFFRACTION17chain 'B' and (resid 497 through 526 )
18X-RAY DIFFRACTION18chain 'B' and (resid 527 through 546 )

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