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- PDB-6czn: Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Com... -

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Basic information

Entry
Database: PDB / ID: 6czn
TitleEstrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with Z2OHTPE and a glucocorticoid receptor-interacting protein 1 NR box II peptide
Components
  • Estrogen receptor
  • GRIP Peptide
KeywordsNUCLEAR PROTEIN / Estrogen Agonist / Breast Cancer / Nuclear Hormone Receptor
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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / locomotor rhythm / mammary gland branching involved in pregnancy / uterus development / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / androgen metabolic process / regulation of lipid metabolic process / steroid hormone mediated signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / Endogenous sterols / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Nuclear signaling by ERBB4 / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / positive regulation of phospholipase C activity / intracellular steroid hormone receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / RNA polymerase II preinitiation complex assembly / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / cellular response to hormone stimulus / protein localization to chromatin / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / Regulation of lipid metabolism by PPARalpha / steroid binding / nitric-oxide synthase regulator activity / ESR-mediated signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / 14-3-3 protein binding / transcription corepressor binding / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / response to progesterone / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / nuclear estrogen receptor binding / transcription coregulator binding / stem cell differentiation / nuclear receptor binding / circadian regulation of gene expression / euchromatin / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / male gonad development / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / 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 / Circadian Clock / sequence-specific double-stranded DNA binding / response to estradiol / PIP3 activates AKT signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / HATs acetylate histones / 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
Similarity search - Function
Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 receptor coactivator, DUF1518 ...Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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
4,4'-[(1R,2R)-1-phenylbutane-1,2-diyl]diphenol / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFanning, S.W. / Han, R. / Maximov, P. / Jordan, V.C. / Greene, G.L.
CitationJournal: To Be Published
Title: Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with Z2OHTPE and a glucocorticoid receptor-interacting protein 1 NR box II peptide
Authors: Fanning, S.W.
History
DepositionApr 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Oct 4, 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
C: GRIP Peptide
D: GRIP Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3966
Polymers61,7594
Non-polymers6372
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-30 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.837, 81.659, 58.381
Angle α, β, γ (deg.)90.00, 111.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 29299.535 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: Protein/peptide GRIP Peptide


Mass: 1579.866 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others) / References: UniProt: Q15596*PLUS
#3: Chemical ChemComp-FNJ / 4,4'-[(1R,2R)-1-phenylbutane-1,2-diyl]diphenol


Mass: 318.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H22O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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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: 1.94 Å3/Da / Density % sol: 36.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 3,350, 200 mM MgCl2, Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.997 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 15539 / % possible obs: 89 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.52
Reflection shellResolution: 2.48→2.54 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.95 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CBZ

6cbz


Resolution: 2.5→46.1 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 709 5.12 %
Rwork0.196 --
obs0.198 13838 84.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3397 0 48 62 3507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023524
X-RAY DIFFRACTIONf_angle_d0.5554768
X-RAY DIFFRACTIONf_dihedral_angle_d13.1621230
X-RAY DIFFRACTIONf_chiral_restr0.021583
X-RAY DIFFRACTIONf_plane_restr0.003583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.69320.2745710.24091340X-RAY DIFFRACTION43
2.6932-2.96420.3021360.23562486X-RAY DIFFRACTION81
2.9642-3.3930.27131850.21943045X-RAY DIFFRACTION99
3.393-4.27440.19811590.17553113X-RAY DIFFRACTION99
4.2744-46.11210.2261580.18263145X-RAY DIFFRACTION99
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)
16.58982.64762.34159.16794.16395.16250.05210.3663-0.6050.3210.8427-1.3728-0.13291.6121-0.91020.35270.11930.03310.9423-0.02580.546912.25921.82855.1768
28.09751.8256-1.99945.32550.88817.5566-0.3311.02830.7628-0.9420.23250.6811-1.0384-0.57730.37140.593-0.043-0.04820.37590.08690.3798-7.72996.997540.602
38.00070.24471.61456.1396-0.57577.9256-0.650.9684-0.7253-0.28810.36710.36120.8784-0.52220.25610.4926-0.11950.07460.3928-0.06810.2034-8.8591-0.125144.4421
44.1525-0.85280.89396.0967-0.47412.8294-0.2273-0.1764-0.5873-0.9094-0.182-0.58831.22560.30580.30290.6822-0.01380.18420.2980.06090.3228-4.51-2.750654.7778
55.96262.4501-1.22668.58434.13253.0942-0.01641.35740.9597-0.79660.19890.1384-0.8559-0.414-0.16510.8480.24130.00140.47260.20310.3599-10.211416.139945.9496
60.1270.9190.36098.2032-0.40956.9411-0.05460.3881-0.1105-0.27460.60951.7385-0.6954-1.4559-0.53190.76580.3338-0.05141.16960.36030.8816-23.169813.568550.3494
76.023-1.31421.04397.28460.61476.7508-0.0561-0.0723-0.13730.1669-0.05490.0325-0.35430.03010.10150.25440.02060.05820.27540.01740.1358-5.19317.705959.0045
85.29061.0151-0.14573.90880.13236.4038-0.1124-0.3622-0.09920.1683-0.101-0.3696-0.08990.58250.15960.2248-0.05890.05560.35110.06110.2365-0.31795.946965.0908
93.1074-2.58361.26425.92650.5062.4651-0.03080.1382-1.7905-0.1430.3554-0.19421.0933-1.1571-0.42440.9035-0.44010.0420.6488-0.01440.8726-17.1551-6.97950.198
100.2728-0.3225-0.05470.7706-0.16030.1416-0.11270.31220.2549-0.18680.4853-0.6399-0.63040.92961.11690.5571-0.744-0.2490.932-0.4520.1692-5.629916.844987.275
117.99350.3435-0.48376.1977-0.85575.81720.0008-0.4886-0.32370.3854-0.03680.470.4928-0.6262-0.05310.257-0.03260.00760.27860.00640.1922-24.61310.467984.6153
125.517-1.0422-0.59516.32110.91065.4850.0909-0.0530.6028-0.0687-0.02170.002-0.7722-0.165-0.02680.17680.00130.03840.22730.04340.2396-18.03739.945877.0124
133.447-3.2049-0.92863.06251.44864.5739-0.7128-0.4592-1.06280.0761-0.3613-0.54041.77060.66150.59340.70970.11920.31270.35970.26420.6325-16.0283-10.364684.9521
141.2991-1.32610.17233.0165-2.47613.204-0.02730.23940.4405-0.47520.56660.5339-0.4911-0.0874-0.42431.5539-0.40590.26530.486-0.14931.1848-24.3197-14.814273.6903
155.61671.47943.43822.751-0.19988.1676-0.49080.9487-0.7181-0.7867-0.1036-0.43111.28581.14030.38280.60710.14310.16080.32530.04270.4972-9.8684-8.413274.717
166.87680.8009-0.28992.18741.88861.81720.1829-0.12890.68470.1189-0.2844-0.2337-0.74611.22010.2060.2698-0.1873-0.00930.5384-0.01230.3138-4.530211.079977.7072
175.7057-0.2957-1.52013.3041-0.813.388-0.15610.0381-0.2904-0.3639-0.0560.34580.4037-0.1720.16050.2454-0.0203-0.05510.3465-0.00460.1633-15.41411.964671.2504
180.5375-0.04640.00322.67441.47010.812-0.10990.0445-0.46940.4668-0.15840.39680.3583-0.09810.37981.93080.2109-0.07120.493-0.25120.82-6.0133-14.727847.8078
193.4319-2.85121.37083.98610.63382.4979-0.4846-0.32540.4582-0.0249-0.18650.1186-0.1587-0.3480.17630.75130.45170.39010.71530.28611.2395-29.227616.730280.6111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 308:322 )A308 - 322
2X-RAY DIFFRACTION2( CHAIN A AND RESID 323:339 )A323 - 339
3X-RAY DIFFRACTION3( CHAIN A AND RESID 340:363 )A340 - 363
4X-RAY DIFFRACTION4( CHAIN A AND RESID 364:394 )A364 - 394
5X-RAY DIFFRACTION5( CHAIN A AND RESID 395:411 )A395 - 411
6X-RAY DIFFRACTION6( CHAIN A AND RESID 412:421 )A412 - 421
7X-RAY DIFFRACTION7( CHAIN A AND RESID 422:468 )A422 - 468
8X-RAY DIFFRACTION8( CHAIN A AND RESID 469:524 )A469 - 524
9X-RAY DIFFRACTION9( CHAIN A AND RESID 525:548 )A525 - 548
10X-RAY DIFFRACTION10( CHAIN B AND RESID 306:322 )B306 - 322
11X-RAY DIFFRACTION11( CHAIN B AND RESID 323:363 )B323 - 363
12X-RAY DIFFRACTION12( CHAIN B AND RESID 364:394 )B364 - 394
13X-RAY DIFFRACTION13( CHAIN B AND RESID 395:411 )B395 - 411
14X-RAY DIFFRACTION14( CHAIN B AND RESID 412:421 )B412 - 421
15X-RAY DIFFRACTION15( CHAIN B AND RESID 422:438 )B422 - 438
16X-RAY DIFFRACTION16( CHAIN B AND RESID 439:496 )B439 - 496
17X-RAY DIFFRACTION17( CHAIN B AND RESID 497:548 )B497 - 548
18X-RAY DIFFRACTION18( CHAIN C AND RESID 688:695 )C688 - 695
19X-RAY DIFFRACTION19( CHAIN D AND RESID 688:696 )D688 - 696

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