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- PDB-4q50: The Estrogen Receptor Alpha Ligand Binding Domain D538G Mutant in... -

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Basic information

Entry
Database: PDB / ID: 4q50
TitleThe Estrogen Receptor Alpha Ligand Binding Domain D538G Mutant in Complex with 4-hydroxytamoxifen
ComponentsEstrogen receptor
Keywordshormone binding protein / Acquired SERM-Resistance / Breast Cancer / Activating Mutation / SERM-ER structure / Alpha Helix / Nuclear hormone 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 / negative regulation of smooth muscle cell apoptotic process / uterus development / 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 / negative regulation of canonical NF-kappaB signal transduction / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / negative regulation of miRNA transcription / ESR-mediated signaling / TBP-class protein binding / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / transcription coregulator binding / transcription corepressor binding / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / Regulation of RUNX2 expression and activity / transcription coactivator binding / male gonad development / nuclear receptor activity / Ovarian tumor domain proteases / positive regulation of fibroblast proliferation / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / 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 / 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 transcription by RNA polymerase II / protein kinase binding / regulation of DNA-templated transcription / 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 / 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 ...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 / 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
4-HYDROXYTAMOXIFEN / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsFanning, S.W. / Greene, G.L.
CitationJournal: Elife / Year: 2016
Title: Estrogen receptor alpha somatic mutations Y537S and D538G confer breast cancer endocrine resistance by stabilizing the activating function-2 binding conformation.
Authors: Fanning, S.W. / Mayne, C.G. / Dharmarajan, V. / Carlson, K.E. / Martin, T.A. / Novick, S.J. / Toy, W. / Green, B. / Panchamukhi, S. / Katzenellenbogen, B.S. / Tajkhorshid, E. / Griffin, P.R. ...Authors: Fanning, S.W. / Mayne, C.G. / Dharmarajan, V. / Carlson, K.E. / Martin, T.A. / Novick, S.J. / Toy, W. / Green, B. / Panchamukhi, S. / Katzenellenbogen, B.S. / Tajkhorshid, E. / Griffin, P.R. / Shen, Y. / Chandarlapaty, S. / Katzenellenbogen, J.A. / Greene, G.L.
History
DepositionApr 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
E: Estrogen receptor
F: Estrogen receptor
G: Estrogen receptor
H: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,15518
Polymers236,8638
Non-polymers3,29210
Water21612
1
A: Estrogen receptor
F: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9914
Polymers59,2162
Non-polymers7752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-8 kcal/mol
Surface area19330 Å2
MethodPISA
2
B: Estrogen receptor
E: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0875
Polymers59,2162
Non-polymers8713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-19 kcal/mol
Surface area18510 Å2
MethodPISA
3
C: Estrogen receptor
G: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9914
Polymers59,2162
Non-polymers7752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-10 kcal/mol
Surface area19040 Å2
MethodPISA
4
D: Estrogen receptor
H: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0875
Polymers59,2162
Non-polymers8713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-18 kcal/mol
Surface area19410 Å2
MethodPISA
5
A: Estrogen receptor
D: Estrogen receptor
F: Estrogen receptor
H: Estrogen receptor
hetero molecules

B: Estrogen receptor
C: Estrogen receptor
E: Estrogen receptor
G: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,15518
Polymers236,8638
Non-polymers3,29210
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Buried area24730 Å2
ΔGint-102 kcal/mol
Surface area70640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.651, 165.244, 191.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 29607.887 Da / Num. of mol.: 8
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.: 8 / Source method: obtained synthetically / Formula: C26H29NO2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.49 Å3/Da / Density % sol: 64.79 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Ammonium Sulfate, 10% glycerol, 100 mM Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K

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Data collection

DiffractionMean temperature: 298.15 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 9874 / % possible obs: 96.7 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 2 / Redundancy: 6.1 %

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.07→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.896 / SU B: 41.693 / SU ML: 0.331 / Cross valid method: THROUGHOUT / σ(F): 5 / ESU R: 3.698 / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28277 3034 5 %RANDOM
Rwork0.21565 ---
all0.1899 ---
obs0.21903 -96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.167 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å2-0 Å20 Å2
2--0.4 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 3.07→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13777 0 242 12 14031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214399
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8152.00119421
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.31351728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.30524.286588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.095152720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9851572
X-RAY DIFFRACTIONr_chiral_restr0.1160.22284
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210281
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.065→3.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 196 -
Rwork0.298 3287 -
obs--79.52 %
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)
11.5290.53920.27893.1926-0.23891.2750.05070.04240.32420.1401-0.04170.19770.0448-0.0188-0.0090.04580.0080.04060.07630.01950.1535-52.901-56.262235.0982
21.7204-0.69460.35644.302-0.54111.8707-0.02050.08110.25990.12060.01470.06470.15650.09770.00580.0310.02680.00960.04590.01890.0778-2.1524-61.794435.0152
31.31960.7568-0.05683.84380.05821.53250.00730.0135-0.250.18720.0365-0.2375-0.0205-0.0305-0.04390.03580.0118-0.0390.0324-0.02560.10215.2034-24.699633.9893
41.1844-0.3557-0.62723.97130.2552.0128-0.00990.0413-0.2051-0.0568-0.0486-0.1343-0.0556-0.12490.05850.0320.0426-0.01710.0619-0.02640.0978-45.386-19.080533.9147
51.48220.4078-0.16821.5805-0.31716.5767-0.16940.09230.061-0.0920.1920.00950.63640.4321-0.02260.2320.08610.04430.08950.01350.02747.7385-78.579918.9091
61.49350.29250.31212.2886-0.0874.6439-0.09110.21330.0351-0.01550.09290.01170.19810.2294-0.00180.08010.0430.01030.0802-0.00240.0454-43.4706-72.729918.5219
71.1440.451-0.00181.69890.44744.3716-0.05080.1405-0.01110.00230.0324-0.0023-0.1867-0.17090.01830.0530.0124-0.02450.1022-0.02170.0201-3.4235-8.679816.8435
80.4788-0.00560.2811.0190.53285.6359-0.01560.0381-0.009-0.2130.01220.0427-0.3757-0.37690.00340.19470.1015-0.07650.0985-0.03650.0487-55.3343-3.370617.0378
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A307 - 545
2X-RAY DIFFRACTION1A1000
3X-RAY DIFFRACTION1A2000 - 2002
4X-RAY DIFFRACTION2B307 - 545
5X-RAY DIFFRACTION2B601
6X-RAY DIFFRACTION2B2000
7X-RAY DIFFRACTION3C306 - 546
8X-RAY DIFFRACTION3C1000
9X-RAY DIFFRACTION3C2000 - 2003
10X-RAY DIFFRACTION4D306 - 545
11X-RAY DIFFRACTION4D1000
12X-RAY DIFFRACTION4D2000
13X-RAY DIFFRACTION5E306 - 545
14X-RAY DIFFRACTION5E1000
15X-RAY DIFFRACTION5E2000
16X-RAY DIFFRACTION6F307 - 545
17X-RAY DIFFRACTION6F1000
18X-RAY DIFFRACTION6G1101
19X-RAY DIFFRACTION7G307 - 546
20X-RAY DIFFRACTION7G1000
21X-RAY DIFFRACTION7G1102
22X-RAY DIFFRACTION8H307 - 546
23X-RAY DIFFRACTION8B602
24X-RAY DIFFRACTION8H601 - 602

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