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

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Basic information

Entry
Database: PDB / ID: 2qgt
TitleCrystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain Complexed to an Ether Estradiol Compound
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION / Protein-Ligand Complex
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 / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / HATs acetylate histones / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / Estrogen-dependent gene expression ...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 / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / HATs acetylate histones / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / Estrogen-dependent gene expression / regulation of epithelial cell apoptotic process / antral ovarian follicle growth / 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 / 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 / locomotor rhythm / mammary gland branching involved in pregnancy / uterus development / negative regulation of smooth muscle cell apoptotic process / aryl hydrocarbon receptor binding / vagina development / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / androgen metabolic process / regulation of glucose 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 / transcription regulator inhibitor activity / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / protein localization to chromatin / steroid binding / 14-3-3 protein binding / positive regulation of adipose tissue development / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / negative regulation of canonical NF-kappaB signal transduction / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / ESR-mediated signaling / response to progesterone / negative regulation of miRNA transcription / TBP-class protein binding / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / nuclear receptor binding / transcription corepressor binding / transcription coregulator binding / negative regulation of smoothened signaling pathway / stem cell differentiation / SUMOylation of intracellular receptors / circadian regulation of gene expression / cellular response to estradiol stimulus / mRNA transcription by RNA polymerase II / euchromatin / circadian rhythm / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / transcription coactivator binding / RNA polymerase II transcription regulator complex / 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 / rhythmic process / response to estradiol / PIP3 activates AKT signaling / positive regulation of cytosolic calcium ion concentration / ATPase binding / regulation of gene expression / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity
Similarity search - Function
Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 ...Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / 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 / Nuclear receptor coactivators bHLH domain / : / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / 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
Chem-EED / 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 / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsNettles, K.W. / Bruning, J.B. / Nowak, J. / Sharma, S.K. / Hahm, J.B. / Shi, Y. / Kulp, K. / Hochberg, R.B. / Zhou, H. / Katzenellenbogen, J.A. ...Nettles, K.W. / Bruning, J.B. / Nowak, J. / Sharma, S.K. / Hahm, J.B. / Shi, Y. / Kulp, K. / Hochberg, R.B. / Zhou, H. / Katzenellenbogen, J.A. / Katzenellenbogen, B.S. / Kim, Y. / Joachmiak, A. / Greene, G.L.
CitationJournal: Nat.Chem.Biol. / Year: 2008
Title: NFkappaB selectivity of estrogen receptor ligands revealed by comparative crystallographic analyses
Authors: Nettles, K.W. / Bruning, J.B. / Gil, G. / Nowak, J. / Sharma, S.K. / Hahm, J.B. / Kulp, K. / Hochberg, R.B. / Zhou, H. / Katzenellenbogen, J.A. / Katzenellenbogen, B.S. / Kim, Y. / Joachmiak, A. / Greene, G.L.
History
DepositionJun 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 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 / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / 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 / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _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)62,5666
Polymers61,9334
Non-polymers6332
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-32.9 kcal/mol
Surface area20480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.171, 83.708, 56.007
Angle α, β, γ (deg.)90.000, 108.450, 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: 29386.609 Da / Num. of mol.: 2 / Fragment: Steroid-binding region, residues 298-554 / Mutation: Y537S
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/peptide Nuclear receptor coactivator 2


Mass: 1579.866 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8BN74, UniProt: Q61026*PLUS
#3: Chemical ChemComp-EED / (9BETA,11ALPHA,13ALPHA,14BETA,17ALPHA)-11-(METHOXYMETHYL)ESTRA-1(10),2,4-TRIENE-3,17-DIOL


Mass: 316.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.09 Å3/Da / Density % sol: 41.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97945 Å
DetectorType: SBC-3 / Detector: CCD / Date: Nov 8, 2004 / Details: mirrors
RadiationMonochromator: Double Crystal Monochromator Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 28301 / Num. obs: 28301 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 20.43 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Χ2: 0.603 / Net I/σ(I): 4.1
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2736 / Rsym value: 0.395 / Χ2: 0.435 / % possible all: 95.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ERD

3erd


Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.91 / SU B: 10.156 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.268 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1431 5.1 %RANDOM
Rwork0.192 ---
obs0.194 28251 96.93 %-
all-28251 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.469 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0.07 Å2
2---0.07 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3978 0 46 134 4158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0214117
X-RAY DIFFRACTIONr_bond_other_d0.0020.022783
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.9935567
X-RAY DIFFRACTIONr_angle_other_deg0.9143.0026778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8535492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.74424.171175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.38615783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8461523
X-RAY DIFFRACTIONr_chiral_restr0.0710.2659
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024367
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02756
X-RAY DIFFRACTIONr_nbd_refined0.2090.2998
X-RAY DIFFRACTIONr_nbd_other0.1970.22787
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21966
X-RAY DIFFRACTIONr_nbtor_other0.0880.22062
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2123
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2880.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3360.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.210
X-RAY DIFFRACTIONr_mcbond_it0.9861.52718
X-RAY DIFFRACTIONr_mcbond_other0.1731.5996
X-RAY DIFFRACTIONr_mcangle_it1.47124003
X-RAY DIFFRACTIONr_scbond_it1.93131742
X-RAY DIFFRACTIONr_scangle_it2.7474.51564
LS refinement shellResolution: 2.15→2.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 74 -
Rwork0.224 1453 -
obs-1527 71.22 %
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)
10.6421-0.1036-0.89221.3706-0.97082.1576-0.0965-0.29180.0148-0.0264-0.019-0.18860.28530.50440.1155-0.01250.0131-0.0130.0870.02770.055629.0915-1.283515.711
20.78920.0736-0.4920.5327-0.20020.7246-0.0045-0.0402-0.00960.0201-0.0169-0.052-0.02170.05040.02140.0002-0.0018-0.00050.0358-0.00010.027621.24792.71888.7762
33.16170.15450.45382.0741-2.77983.8642-0.1120.3657-0.6371-0.08170.3844-0.03110.78730.0039-0.27240.11960.00490.04490.0785-0.01950.148810.9355-16.912917.7511
40.70090.0348-0.88160.1463-0.10361.64420.0357-0.0730.0230.01490.0156-0.02420.00360.0459-0.05130.009-0.00090.00050.07140.00010.017612.43511.645718.058
50.01490.02770.24050.05140.44633.87680.03170.1942-0.2198-0.0313-0.0158-0.12450.1661-0.207-0.01590.06580.03220.04260.051-0.01360.010319.9686-4.6036-6.0924
62.16090.83182.45222.01281.42064.03690.0481-0.1984-0.1879-0.08910.11240.3956-0.1322-0.5255-0.1606-0.02690.01270.00250.10080.03240.1015-15.27330.543815.9351
71.0411-0.16330.25881.5475-0.00280.89560.0652-0.0132-0.0937-0.13990.05970.11250.0439-0.0912-0.12490.0087-0.0208-0.02330.02340.01090.0722-7.3834-3.01788.7574
84.00635.15283.15746.62754.06112.48841.55480.25410.90911.2671-1.9066-1.0371.0394-0.69910.35190.3305-0.02990.02170.2877-0.02110.34494.984419.404915.4352
90.8155-0.21390.40861.2344-0.09091.32450.0345-0.0023-0.0069-0.09030.01410.04190.01320.0219-0.0485-0.0123-0.01840.01580.0374-0.01820.0401-0.27470.429914.2513
103.39980.4091-1.760215.5564-6.76333.67920.7488-0.02350.7261-0.9-0.9189-0.1082-0.3911-0.10290.17010.08860.00710.03750.08580.0510.0252-1.05548.1089-2.024
119.74950.47360.346814.8209-1.6840.36390.09260.19680.1326-0.3258-0.139-1.06060.00150.06240.04650.03830.0460.094-0.0060.00510.094527.9592-16.52463.3809
124.9865-3.2217-4.58042.11732.352514.4957-0.10710.24710.8334-0.2219-0.266-0.0927-1.5287-0.63070.37310.05750.0221-0.08760.06240.02270.2212-13.830816.58044.5882
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA305 - 3359 - 39
2X-RAY DIFFRACTION2AA336 - 45840 - 162
3X-RAY DIFFRACTION3AA459 - 479163 - 183
4X-RAY DIFFRACTION4AA480 - 530184 - 234
5X-RAY DIFFRACTION5AA531 - 548235 - 252
6X-RAY DIFFRACTION6BB305 - 3359 - 39
7X-RAY DIFFRACTION7BB336 - 45840 - 162
8X-RAY DIFFRACTION8BB459 - 472163 - 176
9X-RAY DIFFRACTION9BB473 - 542177 - 246
10X-RAY DIFFRACTION10BB543 - 548247 - 252
11X-RAY DIFFRACTION11CC688 - 6973 - 12
12X-RAY DIFFRACTION12DD687 - 6982 - 13

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