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- PDB-2qzo: Crystal Structure of the Estrogen Receptor Alpha Ligand Binding D... -

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Basic information

Entry
Database: PDB / ID: 2qzo
TitleCrystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain Complexed with WAY-169916
Components
  • (Estrogen receptor) x 2
  • Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION / Protein-Ligand Complex / DNA-binding / Lipid-binding / Metal-binding / Nucleus / Phosphorylation / Receptor / Steroid-binding / Transcription regulation / Zinc-finger
Function / homology
Function and homology information


Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recycling of bile acids and salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts / positive regulation of glucocorticoid receptor signaling pathway / Endogenous sterols / HATs acetylate histones / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 ...Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recycling of bile acids and salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts / positive regulation of glucocorticoid receptor signaling pathway / Endogenous sterols / HATs acetylate histones / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / nuclear glucocorticoid receptor binding / Estrogen-dependent gene expression / nuclear retinoic acid receptor binding / positive regulation of female receptivity / nuclear thyroid hormone receptor binding / 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 / negative regulation of smooth muscle cell apoptotic process / 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 / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / Nuclear signaling by ERBB4 / positive regulation of phospholipase C activity / DNA polymerase binding / nuclear retinoid X receptor binding / intracellular steroid hormone receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / RNA polymerase II preinitiation complex assembly / 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 / 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 / nuclear receptor coactivator activity / 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 / mRNA transcription by RNA polymerase II / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / beta-catenin binding / Nuclear Receptor transcription pathway / circadian rhythm / 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 / 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
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
Chem-KN1 / Estrogen receptor / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.72 Å
AuthorsBruning, J.B. / Gil, G. / Nowak, J. / Katzenellenbogen, J. / Nettles, K.W.
CitationJournal: Nat.Chem.Biol. / Year: 2010
Title: Coupling of receptor conformation and ligand orientation determine graded activity.
Authors: Bruning, J.B. / Parent, A.A. / Gil, G. / Zhao, M. / Nowak, J. / Pace, M.C. / Smith, C.L. / Afonine, P.V. / Adams, P.D. / Katzenellenbogen, J.A. / Nettles, K.W.
History
DepositionAug 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...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.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: 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
C: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8306
Polymers62,1614
Non-polymers6692
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-40.6 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.806, 82.029, 58.517
Angle α, β, γ (deg.)90.000, 109.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Estrogen receptor / / ER / Estradiol receptor / ER-alpha


Mass: 29462.727 Da / Num. of mol.: 1 / Fragment: STEROID-BINDING REGION, RESIDUES 298-554
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: P03372
#2: Protein Estrogen receptor /


Mass: 29538.844 Da / Num. of mol.: 1 / Fragment: STEROID-BINDING REGION, RESIDUES 298-554
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: P03372
#3: Protein/peptide Nuclear receptor coactivator 2 /


Mass: 1579.866 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide is naturally found in Mus Musculus (mouse).
Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8BN74, UniProt: Q61026*PLUS
#4: Chemical ChemComp-KN1 / 4-[1-allyl-7-(trifluoromethyl)-1H-indazol-3-yl]benzene-1,3-diol


Mass: 334.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H13F3N2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 3, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.72→15 Å / Num. obs: 48276 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 30.73 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Χ2: 1.083 / Net I/σ(I): 27.9
Reflection shellResolution: 1.72→1.86 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 6.57 / Num. unique all: 3762 / Rsym value: 0.176 / Χ2: 1.264 / % possible all: 82.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementStarting model: PDB entry 3ERD

3erd


Resolution: 1.72→9.91 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.324 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.126 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2446 5.1 %RANDOM
Rwork0.178 ---
obs0.18 48124 91.58 %-
all-48124 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.541 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.02 Å2
2---0.01 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.72→9.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3816 0 48 422 4286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214034
X-RAY DIFFRACTIONr_bond_other_d0.0020.022676
X-RAY DIFFRACTIONr_angle_refined_deg1.4892.0015485
X-RAY DIFFRACTIONr_angle_other_deg0.9933.0016584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.045509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.34524.172163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4915752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7941521
X-RAY DIFFRACTIONr_chiral_restr0.1510.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024345
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02736
X-RAY DIFFRACTIONr_nbd_refined0.2380.21088
X-RAY DIFFRACTIONr_nbd_other0.2110.22830
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21894
X-RAY DIFFRACTIONr_nbtor_other0.1120.22050
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2292
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5330.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3340.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3830.218
X-RAY DIFFRACTIONr_mcbond_it0.9911.52545
X-RAY DIFFRACTIONr_mcbond_other0.2411.5983
X-RAY DIFFRACTIONr_mcangle_it1.50823962
X-RAY DIFFRACTIONr_scbond_it2.50431698
X-RAY DIFFRACTIONr_scangle_it3.654.51503
LS refinement shellResolution: 1.72→1.764 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 105 -
Rwork0.223 2052 -
all-2157 -
obs-2157 56.55 %
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)
11.6930.25981.06981.3430.03582.7866-0.12440.1756-0.0284-0.23090.09080.0065-0.04920.00610.03360.0968-0.01680.03110.08870.00230.049312.60860.046-1.7071
22.00920.17-0.41330.9055-0.1220.9080.0488-0.08650.00850.0881-0.02910.038-0.0126-0.0289-0.01970.06810.006200.0889-0.00490.06354.1001-0.38922.0502
338.65587.607112.326724.396622.824822.10240.91941.0895-2.2411-0.1467-0.35750.10630.24160.1157-0.56190.3151-0.0214-0.00440.244-0.06160.2438.0366-17.1906-11.4447
46.434-2.43576.960221.07940.007913.71730.0428-0.25910.79590.0837-0.49481.3193-0.0084-0.57630.4520.04160.03650.08230.0606-0.11180.2699-6.597416.651925.7372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA305 - 5499 - 253
2X-RAY DIFFRACTION2BB306 - 54910 - 253
3X-RAY DIFFRACTION3CC687 - 6952 - 10
4X-RAY DIFFRACTION4DD688 - 6963 - 11

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