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- PDB-6vgh: Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant In Com... -

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Basic information

Entry
Database: PDB / ID: 6vgh
TitleEstrogen Receptor Alpha Ligand Binding Domain Y537S Mutant In Complex with Lasofoxifene
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / Breast Cancer / Steroid Receptor / Activating Mutant / Selective Estrogen Receptor Modulator / Antiestrogen / Lasofoxifene
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 / prostate epithelial cord elongation / epithelial cell development / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / androgen metabolic process / TFIIB-class transcription factor binding / steroid hormone mediated signaling pathway / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / positive regulation of phospholipase C activity / intracellular steroid hormone receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / steroid binding / nitric-oxide synthase regulator activity / ESR-mediated signaling / 14-3-3 protein binding / transcription corepressor binding / negative regulation of miRNA transcription / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of nitric-oxide synthase activity / euchromatin / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / nuclear receptor activity / positive regulation of nitric oxide biosynthetic process / positive regulation of DNA-binding transcription factor activity / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / sequence-specific double-stranded DNA binding / response to estradiol / PIP3 activates AKT signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / positive regulation of cytosolic calcium ion concentration / fibroblast proliferation / regulation of inflammatory response / 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 / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
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
Chem-C3D / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFanning, S.W. / Greene, G.L.
CitationJournal: To Be Published
Title: Ligand Binding Domain
Authors: Fanning, S.W.
History
DepositionJan 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: 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)60,8954
Polymers60,0682
Non-polymers8272
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-9 kcal/mol
Surface area20630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.692, 58.692, 276.475
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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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
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-C3D / (5R,6S)-6-PHENYL-5-[4-(2-PYRROLIDIN-1-YLETHOXY)PHENYL]-5,6,7,8-TETRAHYDRONAPHTHALEN-2-OL / Lasofoxifene / Lasofoxifene


Mass: 413.551 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H31NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3,350, Tris pH 7.5, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.987 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 28416 / % possible obs: 90.9 % / Redundancy: 3 % / Biso Wilson estimate: 24.1370617079 Å2 / CC1/2: 0.925 / Rpim(I) all: 0.07 / Net I/σ(I): 837
Reflection shellResolution: 2.09→2.14 Å / Mean I/σ(I) obs: 3.6 / Num. unique obs: 3720 / CC1/2: 0.749

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6V8T

6v8t


Resolution: 2.1→28.71 Å / SU ML: 0.2856 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 26.82
RfactorNum. reflection% reflection
Rfree0.274 1389 4.9 %
Rwork0.2158 --
obs0.2185 28411 90.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.9 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3570 0 62 256 3888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001979693034593740
X-RAY DIFFRACTIONf_angle_d0.6811264471525059
X-RAY DIFFRACTIONf_chiral_restr0.0246954865463604
X-RAY DIFFRACTIONf_plane_restr0.00203635024741622
X-RAY DIFFRACTIONf_dihedral_angle_d13.82859410171368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1740.29431070.24952571X-RAY DIFFRACTION86.1647361647
2.174-2.2610.3442785875921480.2821436972762612X-RAY DIFFRACTION88.1507505589
2.261-2.36380.2927256207171540.2403516348182676X-RAY DIFFRACTION90.9383033419
2.3638-2.48840.3089336987541200.2218676141162791X-RAY DIFFRACTION93.8426821406
2.4884-2.64420.2576156027721530.2289558938332785X-RAY DIFFRACTION94.1364947132
2.6442-2.84820.2945535091761490.2306401432962737X-RAY DIFFRACTION92.4703620634
2.8482-3.13450.3157973183351490.2198830569562798X-RAY DIFFRACTION94.0631982126
3.1345-3.58730.2700800602341400.2069436035792717X-RAY DIFFRACTION91.0162472125
3.5873-4.51680.2327973489761340.1797459606772640X-RAY DIFFRACTION88.1194409149
4.5168-28.70.2489050484141350.2074765359482695X-RAY DIFFRACTION90.2423469388
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)
13.90639966709-1.02196760289-0.1441993514772.38850604470.3432161124081.7606637866-0.03718235838870.06008481928390.636707686214-0.110294440015-0.034823646507-0.268786354322-0.859824572693-0.2350304588730.05965586109130.6491390043440.106976336453-0.130014301820.2616874606060.06627554977260.408400228861-36.706391273538.8381304283-19.1570097094
22.46034949751-0.8519978177-0.1009232100561.54647781499-0.05275021656121.81007292932-0.2015733067350.3462888686690.3012556411060.2546451911860.1452055337050.0882523715698-0.653073514457-0.230642656360.0421413848880.4046669053060.302599562102-0.00141130399370.1050489149160.004712420226410.236848512966-40.359044395130.1286921161-20.0911420118
32.70653416653-2.806742864540.223102669827.28452444171.297448251163.22602388972-0.416579058966-0.210572498402-0.734332795951.044687586180.2789927644940.7633250167030.473602674099-0.3530674683670.1075931026870.6763523430140.1957017569380.1617258650440.4627480542830.03606365562840.452992895892-47.064989725322.9242359068-2.80411929583
44.729135990741.59374982534-1.596491477126.069252518-1.255185811671.959498076090.028828348787-0.527685219551-0.1234103604530.410040255488-0.1722350727090.0870502172173-0.1751775069860.2068317434520.1599751329390.5854218417590.156319669932-0.02649136235390.2873594662120.01130861875310.197979754729-34.137484511323.6252305879-5.72019451541
53.400890656860.4464217131161.603187443822.796745553421.399457075856.1505237377-0.1194720021190.3511728156320.363405760881-0.179414755296-0.106446854242-0.316991480724-0.6356814730340.3504708896860.2226206231780.30827556240.0355970186595-0.002569420112690.1824576453290.130152736940.330079335776-24.427947541728.5774615154-25.0977194983
69.341843481933.254062183970.6485759253923.93203946013-0.4060167784452.03165741565-0.0947744274125-0.300297946529-0.6749425502510.183418662735-0.0554211031348-0.3673083479740.02175844406450.1904595117560.1511185219450.3491949274690.10266998107-0.007142087121370.1371520694050.03491716755990.20433451311-28.51197704821.139236017-15.0179328192
70.765290437206-1.68472444091.279157092162.01939062029-2.842490207162.213833388110.2552036761460.4315799055150.07600237947820.272417145538-0.1169026370851.36795873338-0.194886917342-0.541954573195-0.1650553942370.4784159146450.2796227867580.04986618376820.872344943881-0.03490218176810.438176788283-47.493524639529.6530587659-33.8815393683
83.897834363511.171073531020.001663348125494.100061257670.02225222052761.38064450441-0.3176119801780.295867933677-0.13563578889-0.1031884666070.140771953576-0.2984376126890.4945521390780.570523611120.1347078615830.5060405663510.2146458302120.02989664545210.2910951317130.04655422388940.216949372204-19.5070579358-3.16741707156-18.1758708636
91.2133656279-0.252909828306-0.1262981332073.71070186576-0.1201145503122.371575943080.1179894267140.222532070579-0.0731325646816-0.298735421517-0.2271228065930.07625196353180.2392919014140.08424414596360.1163124498480.358122740170.176017524165-0.006592462620430.1768488725850.01092558114980.240158686505-25.55382026212.49861711647-21.1077273761
102.033847614210.5135409934810.7211899285083.698094392870.3852136003782.473199070780.02843369493170.1161547174290.1029836411670.0839154394417-0.194602811791-0.1967687059090.1067412185330.266564377840.156879855340.2297579489140.127814023329-0.009390836917650.2038289769040.04360724690360.221044427338-21.920528048412.5604433282-16.7366270676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 307 through 341 )
2X-RAY DIFFRACTION2chain 'A' and (resid 342 through 407 )
3X-RAY DIFFRACTION3chain 'A' and (resid 408 through 422 )
4X-RAY DIFFRACTION4chain 'A' and (resid 423 through 437 )
5X-RAY DIFFRACTION5chain 'A' and (resid 438 through 496 )
6X-RAY DIFFRACTION6chain 'A' and (resid 497 through 525 )
7X-RAY DIFFRACTION7chain 'A' and (resid 526 through 550 )
8X-RAY DIFFRACTION8chain 'B' and (resid 307 through 363 )
9X-RAY DIFFRACTION9chain 'B' and (resid 364 through 421 )
10X-RAY DIFFRACTION10chain 'B' and (resid 422 through 545 )

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