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- PDB-7ndo: ER-PRS*(-) (L536S, L372R) in complex with raloxifene -

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Basic information

Entry
Database: PDB / ID: 7ndo
TitleER-PRS*(-) (L536S, L372R) in complex with raloxifene
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / human estrogen receptor alpha / hERa-LBD / raloxifene / ligand binding domain / ER
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 / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / 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 / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor ...Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / 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 / 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
RALOXIFENE / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKriegel, M. / Muller, Y.A.
CitationJournal: Sci Rep / Year: 2021
Title: A PROSS-designed extensively mutated estrogen receptor alpha variant displays enhanced thermal stability while retaining native allosteric regulation and structure.
Authors: Kriegel, M. / Wiederanders, H.J. / Alkhashrom, S. / Eichler, J. / Muller, Y.A.
History
DepositionFeb 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_prop.value
Revision 1.2Jan 31, 2024Group: 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
A: Estrogen receptor
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,49915
Polymers56,9492
Non-polymers1,55013
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-15 kcal/mol
Surface area20440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.581, 51.787, 57.513
Angle α, β, γ (deg.)97.839, 113.516, 110.417
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 28474.348 Da / Num. of mol.: 2
Mutation: M315I, V316I, D321E, T334S, S341Y, R363K, T371S, L372R, C381S, E397D, N407D, N413E, C417S, S433E, M437E, N439K, G442R, S450A, E471N, D473E, H474K, V478M, T485A, H488W, L489Y, A493S, T496S, C530S, 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-RAL / RALOXIFENE


Mass: 473.583 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H27NO4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.07 Å3/Da / Density % sol: 40.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion
Details: 0.2 M sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 23, 2020
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.6→42.8 Å / Num. obs: 56359 / % possible obs: 93.56 % / Redundancy: 3.7 % / Biso Wilson estimate: 25.88 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05248 / Rpim(I) all: 0.03125 / Rrim(I) all: 0.06115 / Net I/σ(I): 11.81
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.287 / Num. unique obs: 5535 / CC1/2: 0.478 / CC star: 0.804 / Rpim(I) all: 0.7659 / Rrim(I) all: 1.499 / % possible all: 92.11

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
MxCuBEdata collection
XDSdata processing
PHENIX1.17.1_3660phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QXS

2qxs


Resolution: 1.6→42.8 Å / SU ML: 0.2288 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 27.3991
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 1284 2.28 %1284
Rwork0.1852 55068 --
obs-56352 93.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.14 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3801 0 103 289 4193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00274055
X-RAY DIFFRACTIONf_angle_d0.51775476
X-RAY DIFFRACTIONf_chiral_restr0.0316611
X-RAY DIFFRACTIONf_plane_restr0.0026676
X-RAY DIFFRACTIONf_dihedral_angle_d17.34581555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6570.42681370.37435535X-RAY DIFFRACTION92.11
1.74-1.830.26541340.27316191X-RAY DIFFRACTION94.53
1.83-1.950.25611560.23016135X-RAY DIFFRACTION93.95
1.95-2.10.20831380.20285998X-RAY DIFFRACTION91.76
2.1-2.310.19831420.18056229X-RAY DIFFRACTION95.05
2.31-2.640.1921390.17436020X-RAY DIFFRACTION92.41
2.64-3.330.20471530.18126302X-RAY DIFFRACTION96.21
3.33-42.80.15141450.15436123X-RAY DIFFRACTION93.62
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)
14.011677382380.869428295084-2.843715197753.62917223147-3.242913696614.022222094240.596418184482-1.401022249840.2543029824581.35628281087-0.3085325433110.4324466799440.349792818845-0.902808115815-0.1544833965780.420746202265-0.1439642004870.03678190322740.595512017371-0.01800659727850.31210736680512.76874385421.4749346350444.6466577182
24.919912167012.950844030710.4633760725577.29298483583-0.4905694460942.87835550224-0.1297608731160.3452752229090.19159704745-0.3806381761360.0334999230466-0.344188166799-0.3318382511420.2966470601370.05211659711240.4085864852730.00637354157954-0.05281629031880.363224294225-0.01165541487810.26171609765533.792493653616.259324328337.7432440879
33.33745021391-1.930714271381.374840209885.47837360616-2.605113677695.800700253230.162565052275-0.0426701864238-0.321244626920.0331617662452-0.210485876506-0.5253454722910.3264760611320.1662089698210.01934554932840.285712553801-0.0142965840839-0.1140027131240.191571655016-0.02807813686010.29295804116228.38753532580.32827081407735.6353793731
45.558095172691.566217984294.256424964144.612705482671.343101135165.4552657158-0.370669541144-0.006896092814380.471416104835-0.124065475885-0.1470771023710.271939830259-0.7778694329160.02216415471770.458674280490.551669935480.0544444458422-0.1301572563530.232346778108-0.03370481693480.28068514166124.611204916322.164812543730.3856732444
57.48876446371-5.264603831441.235898863176.109189248670.5314686179145.26016995486-0.07146460424130.7400909578030.3212212757970.0980969552672-1.06586892252-1.83420393244-0.06398797736961.641206100581.068319277780.993631428342-0.215481436656-0.0656555658910.821348727220.2005116007260.72757224998134.420228308121.786580858620.2017795483
62.395657582091.13112842353-0.4664796084416.52999525131-0.3972433961083.88127966490.06172162160140.01229823085880.025942000005-0.491080314686-0.15529630305-0.0638823807482-0.205486584902-0.1316360193620.01480507530230.311791418790.0234715827598-0.08257047661320.2483698577-0.07163959057080.20410441804320.73502849245.9775978970928.3883225297
76.06630123664-3.195050096280.4872995416833.31026243370.02811965618445.85986505970.074976713787-0.265826033179-0.5214601154040.427679260802-0.03892851040490.09445495292560.674097877324-0.247281036137-0.01138802825020.382434661694-0.0865698349703-0.05753603432280.331024296559-0.03194226341480.42728871203113.4885758937-6.1078699067335.0865215425
85.959518371543.12884649153-1.427715005475.478266530080.1849070861962.77751842067-0.252322576922-0.3761525971260.370973238142-0.419261078706-0.0138511210473-0.109250473159-0.2014496648460.06883244416360.2643122548490.332973152910.0390788725461-0.03932299977830.221574958678-0.03003596006750.1813554858220.42989547063.7416258003523.2876943131
92.447330175833.27902578592-2.932103710576.64046721117-6.803405636727.188468383740.4881705420370.530424661254-0.280068185906-0.206521160988-0.5399585916-1.04725423492-0.5409862726240.6067717455680.01373954561610.590426762019-0.02510838221560.04548823482660.9895193047140.08086446772521.1816070454943.31943863747.5906005037129.4291744737
102.747117273853.82572495886-4.040942231186.7349333013-3.438316144739.83082401668-0.878234588886-0.1011044978630.2495937888181.080373634050.225528406334-1.35414707596-0.176690078768-0.02064149807060.7938235278580.5825676910690.0748327667249-0.2795714109310.516994756742-0.01622162894830.84027023760638.3407959622-1.8369601664543.27507346
110.469642561545-0.202740554810.3896540719972.20097353489-1.664696795061.40801155293-0.01487410897710.246398521163-0.372301162086-0.0434775534879-0.1816875959550.503342911548-0.180421247364-0.6292365721060.07126725718750.2157174775430.0201105756424-0.08462107398050.401551702466-0.1122657691780.3651518616463.98436734608-8.93134354587.47783732256
122.18327832274-0.5531637766130.6577721111962.257094406960.6601948284572.197350292170.02246932620810.167992486237-0.0442659203939-0.128836655812-0.0293079402978-0.0402689615243-0.03473858829850.1126056429650.0003302732977540.166590105307-0.0125060938353-0.03948473972550.213202517629-0.01826251986240.20052522265926.0789329164-10.57567726564.65404429747
139.834209843250.183494816224-2.663390998791.533347422120.7744909703773.80221760528-0.0188939351401-0.344184003532-0.1954758205990.1665365735290.122201668501-0.1585191166460.06993321951080.375789945247-0.09184144396930.2715086366810.037488847924-0.08402225979950.3376774543630.01310901638880.29957525556833.1393319661-14.894994814918.3263939409
142.97336143131-0.917159350874-0.02374489069132.63828145024-1.239956907713.236557103550.0796269851126-0.06074589788390.134515658570.450394851055-0.174747679550.00619753606615-0.4869352356570.0739560934250.1026507005770.292724471423-0.0300451831655-0.04030528010380.288193201096-0.05330216456770.27056959635515.8588400551-3.4989253680214.0028003828
154.041156995154.30027524523-4.110629846845.08062406112-4.124235129485.38185896140.2229419661720.1080649854550.3325782050990.151915253596-0.04794076511910.424658621519-0.656241961148-0.202502620078-0.1767164109170.3018066923210.0213806597327-0.08117908785010.343405046704-0.0689815238360.3967349164287.051982380050.46218802185815.1029433866
165.402125950062.10178235492-3.584722095662.87919914816-1.111634337694.721101448150.000591005284586-0.0449086432155-0.01845988717170.254741416195-0.00142092722142-0.1841758361390.04435576605910.06300575057160.03456331539920.3049686548050.00627592653902-0.08992307778320.29067562384-0.02662792981420.31570346636722.7895545553-5.4332198297520.3057672974
171.52781662868-2.671260751431.757321117336.5933823113-1.934435146547.57701268634-0.04527095273130.7989054785670.82389654781-0.435929174321-0.293537311778-1.08243721623-0.1751150414791.245654367340.355002164880.673688856632-0.0763393298087-0.06203070061070.5660996690310.08511140278970.64030233502727.46595618522.68644450031-2.88392013995
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 311 through 321 )
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 363 )
3X-RAY DIFFRACTION3chain 'A' and (resid 364 through 394 )
4X-RAY DIFFRACTION4chain 'A' and (resid 395 through 411 )
5X-RAY DIFFRACTION5chain 'A' and (resid 412 through 421 )
6X-RAY DIFFRACTION6chain 'A' and (resid 422 through 468 )
7X-RAY DIFFRACTION7chain 'A' and (resid 469 through 496 )
8X-RAY DIFFRACTION8chain 'A' and (resid 497 through 527 )
9X-RAY DIFFRACTION9chain 'A' and (resid 528 through 536 )
10X-RAY DIFFRACTION10chain 'A' and (resid 537 through 547 )
11X-RAY DIFFRACTION11chain 'B' and (resid 310 through 321 )
12X-RAY DIFFRACTION12chain 'B' and (resid 322 through 411 )
13X-RAY DIFFRACTION13chain 'B' and (resid 412 through 437 )
14X-RAY DIFFRACTION14chain 'B' and (resid 438 through 465 )
15X-RAY DIFFRACTION15chain 'B' and (resid 466 through 496 )
16X-RAY DIFFRACTION16chain 'B' and (resid 497 through 528 )
17X-RAY DIFFRACTION17chain 'B' and (resid 529 through 547 )

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