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- PDB-1a52: ESTROGEN RECEPTOR ALPHA LIGAND-BINDING DOMAIN COMPLEXED TO ESTRADIOL -

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Basic information

Entry
Database: PDB / ID: 1a52
TitleESTROGEN RECEPTOR ALPHA LIGAND-BINDING DOMAIN COMPLEXED TO ESTRADIOL
ComponentsESTROGEN RECEPTOR
KeywordsRECEPTOR / ESTROGEN / LIGAND / TRANSCRIPTION REGULATION
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 / TBP-class protein binding / negative regulation of miRNA transcription / 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 / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / 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 / fibroblast proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / 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
: / ESTRADIOL / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsTanenbaum, D.M. / Wang, Y. / Sigler, P.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Crystallographic comparison of the estrogen and progesterone receptor's ligand binding domains.
Authors: Tanenbaum, D.M. / Wang, Y. / Williams, S.P. / Sigler, P.B.
History
DepositionFeb 19, 1998Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,74210
Polymers59,0162
Non-polymers1,7278
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-53 kcal/mol
Surface area22040 Å2
MethodPISA
2
A: ESTROGEN RECEPTOR
B: ESTROGEN RECEPTOR
hetero molecules

A: ESTROGEN RECEPTOR
B: ESTROGEN RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,48420
Polymers118,0314
Non-polymers3,45316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area14860 Å2
ΔGint-159 kcal/mol
Surface area39690 Å2
MethodPISA
3
A: ESTROGEN RECEPTOR
hetero molecules

A: ESTROGEN RECEPTOR
hetero molecules

B: ESTROGEN RECEPTOR
hetero molecules

B: ESTROGEN RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,48420
Polymers118,0314
Non-polymers3,45316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_546y+2/3,x-2/3,-z+4/31
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation8_545-y+2/3,x-y-2/3,z+1/31
Buried area10980 Å2
ΔGint-120 kcal/mol
Surface area43570 Å2
MethodPISA
4
A: ESTROGEN RECEPTOR
hetero molecules

B: ESTROGEN RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,74210
Polymers59,0162
Non-polymers1,7278
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area4130 Å2
ΔGint-55 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.000, 147.000, 168.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-555-

HOH

21A-564-

HOH

31B-25-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper: (Code: given
Matrix: (-0.966537, -0.255999, 0.016449), (-0.2533, 0.962554, 0.096583), (-0.040599, 0.089184, -0.995189)
Vector: 195.105, 17.241, 171.595)

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Components

#1: Protein ESTROGEN RECEPTOR / ERLBD


Mass: 29507.809 Da / Num. of mol.: 2 / Fragment: LIGAND-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: ESR / Plasmid: PET223D / Gene (production host): ERG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLSS / References: UniProt: P03372
#2: Chemical ChemComp-EST / ESTRADIOL


Mass: 272.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24O2
#3: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Au
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.97 Å3/Da / Density % sol: 58.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: WELL: 100 MM TRIS PH 7.6 480 MM MGCL2 10 MM MGOAC2 10% ETHYLENE GLYCOL 5% PEG 4000. PROTEIN STOCK: 18 MG/ML ERLBD 25 MM TRIS PH 7.4 200 MM NACL 1 MM EDTA 1 MM DTT 20 MICROMOLAR ESTRADIOL 0. ...Details: WELL: 100 MM TRIS PH 7.6 480 MM MGCL2 10 MM MGOAC2 10% ETHYLENE GLYCOL 5% PEG 4000. PROTEIN STOCK: 18 MG/ML ERLBD 25 MM TRIS PH 7.4 200 MM NACL 1 MM EDTA 1 MM DTT 20 MICROMOLAR ESTRADIOL 0.1% BETA-OCTYL GLUCOSIDE AT 18 CELSIUS., vapor diffusion - hanging drop, temperature 291K
PH range: 7.4-7.6
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMTris1reservoirpH7.6
2480 mM1reservoirMgCl2
310 mMmagnesium acetate1reservoir
410 %ethylene glycol1reservoir
55 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.0397
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1997 / Details: SPHERICAL MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0397 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 33401 / % possible obs: 99.1 % / Rmerge(I) obs: 0.068 / Rsym value: 0.075 / Net I/σ(I): 19.3
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.329 / % possible all: 98.6

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.3Arefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.8→50 Å / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1539 10 %RANDOM
Rwork0.223 ---
obs0.223 15339 87.7 %-
Solvent computationSolvent model: DENSITY MODIFICATION / Bsol: -9999 Å2 / ksol: 999 e/Å3
Displacement parametersBiso mean: 25.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.57 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3827 0 46 30 3903
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.68
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.01
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.934
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)Weight Biso Weight position
11RESTRAINTS3.45050.11215100
223.55690.1709550
332.70520.1972830
440.39740.1585830
LS refinement shellResolution: 2.8→2.83 Å / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.4047 38 10 %
Rwork0.3183 405 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PACNS_TOPPAR:PROTEIN_REP.TOP
X-RAY DIFFRACTION2CNS_TOPPAR:WATER_REP.PARACNS_TOPPAR:WATER_REP.TOP
X-RAY DIFFRACTION3ESTRO.PARAESTRO.TOPO
X-RAY DIFFRACTION4AUCL4.PARAUCL4.TOP
Software
*PLUS
Name: CNS DEVELOPMENT / Version: VERSION 0.3A / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.4322 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0014
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.01868
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93458

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