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

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Basic information

Entry
Database: PDB / ID: 2qxm
TitleCrystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain Complexed to Burned Meat Compound PhIP
Components
  • Estrogen receptor
  • 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 / 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 / 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 / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / 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 / uterus development / mammary gland branching involved in pregnancy / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / steroid hormone receptor signaling pathway / regulation of lipid metabolic process / androgen metabolic process / regulation of glucose metabolic process / cellular response to estrogen stimulus / mammary gland alveolus development / estrogen response element binding / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / estrogen receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / positive regulation of adipose tissue development / steroid binding / 14-3-3 protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / peroxisome proliferator activated receptor signaling pathway / TBP-class protein binding / regulation of cellular response to insulin stimulus / nitric-oxide synthase regulator activity / positive regulation of nitric-oxide synthase activity / negative regulation of miRNA transcription / ESR-mediated signaling / positive regulation of DNA-binding transcription factor activity / transcription coregulator binding / response to progesterone / transcription corepressor binding / nuclear receptor binding / nuclear estrogen receptor binding / negative regulation of DNA-binding transcription factor activity / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / transcription coactivator binding / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / response to estrogen / nuclear receptor activity / circadian rhythm / positive regulation of fibroblast proliferation / male gonad development / 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 / response to estradiol / PIP3 activates AKT signaling / ATPase binding / regulation of gene expression / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / 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 / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / Extra-nuclear estrogen signaling / calmodulin binding
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 / 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
2-AMINO-1-METHYL-6-PHENYLIMIDAZO[4,5-B]PYRIDINE / 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 / molecular replacement / Resolution: 2.3 Å
AuthorsNettles, K.W. / Bruning, J.B. / Gil, G. / Nowak, J. / Sharma, S.K. / Hahm, J.B. / Shi, Y. / Kulp, K. / Hochberg, R.B. / Zhou, H. ...Nettles, K.W. / Bruning, J.B. / Gil, G. / 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
DepositionAug 12, 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 25, 2017Group: Refinement description / Source and taxonomy / Category: pdbx_entity_src_syn / software
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._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 / _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_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
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3816
Polymers61,9334
Non-polymers4492
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-19.3 kcal/mol
Surface area20530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.965, 83.703, 58.427
Angle α, β, γ (deg.)90.00, 108.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: 306 - 549 / Label seq-ID: 10 - 253

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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
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-PIQ / 2-AMINO-1-METHYL-6-PHENYLIMIDAZO[4,5-B]PYRIDINE


Mass: 224.261 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 41.23 %
Crystal growTemperature: 298 K / pH: 8.5
Details: 0.2M Magnesium chloride hexahydrate, 0.1M Tris 8.5, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97946
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: 2.3→12 Å / Num. obs: 20199 / % possible obs: 88.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 46.85 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 16.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 3.73 / Rsym value: 0.241 / % possible all: 86.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ERD

3erd


Resolution: 2.3→11.96 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.879 / SU B: 30.536 / SU ML: 0.323 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.753 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1040 5.2 %RANDOM
Rwork0.273 ---
obs0.274 20138 88.5 %-
all-20138 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å2-0.34 Å2
2---0.45 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.3→11.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3927 0 34 4 3965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214075
X-RAY DIFFRACTIONr_bond_other_d0.010.022712
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9925516
X-RAY DIFFRACTIONr_angle_other_deg2.7393.0026659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2945504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00224.217166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.72915769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6851520
X-RAY DIFFRACTIONr_chiral_restr0.0930.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024379
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02753
X-RAY DIFFRACTIONr_nbd_refined0.240.21085
X-RAY DIFFRACTIONr_nbd_other0.2560.22796
X-RAY DIFFRACTIONr_nbtor_refined0.1950.22004
X-RAY DIFFRACTIONr_nbtor_other0.10.22270
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.279
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0480.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4010.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined1.0980.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it10.1751.52562
X-RAY DIFFRACTIONr_mcbond_other1.3671.51000
X-RAY DIFFRACTIONr_mcangle_it11.03124007
X-RAY DIFFRACTIONr_scbond_it14.83731705
X-RAY DIFFRACTIONr_scangle_it15.0564.51501
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3004 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.480.05
tight thermal3.390.5
LS refinement shellResolution: 2.3→2.35 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 63 -
Rwork0.344 1309 -
obs--84.48 %
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)
13.4455-1.84792.46351.9612-1.61973.46830.1360.6101-0.2034-0.2104-0.05920.0602-0.02680.3234-0.07680.1521-0.04150.04070.0907-0.06140.121416.78470.3678-9.5846
20.6894-1.64130.45093.9079-1.04642.3635-0.1180.1387-0.00930.00120.1956-0.2223-0.05370.0551-0.07760.1345-0.02280.04230.1395-0.01520.095611.9843-2.3802-6.5988
31.9983-0.5733-1.73784.86181.07271.58150.10770.18370.1213-0.6314-0.07490.405-0.0172-0.1777-0.03280.23170.0405-0.01240.01890.09270.20034.061213.3468-2.4282
40.98850.75190.63821.40870.20731.2350.0203-0.040.0136-0.0026-0.07550.06130.2598-0.03590.05530.1387-0.0140.05840.138-0.01920.101820.9796-5.52926.7952
51.3455-0.01590.60290.53410.21881.15120.04140.05250.0506-0.0579-0.11010.08610.0234-0.18380.06870.1510.01410.01420.09170.00490.11264.4469-0.61580.5593
60.60750.0536-0.53790.108-0.10750.51120.0566-0.42660.10740.205-0.07060.14820.06610.01060.0140.1688-0.02740.03460.1358-0.00430.1242-0.6169-2.048529.7288
70.42070.3191-0.21041.1899-0.07680.5170.025-0.0277-0.02420.0577-0.0501-0.00290.01650.02170.02510.14060.00760.05280.09920.0170.10673.4282-2.300722.8317
810.7975-3.97670.31141.8535-1.22113.15641.3180.4621.67630.2473-0.8221-0.5577-0.4449-1.2631-0.49590.47160.11460.13170.21970.07360.23911.904619.008614.4468
92.579-0.14870.28710.039-0.17030.80950.0343-0.1430.0195-0.0255-0.134-0.04960.09670.0410.09980.08880.0110.02170.1101-0.00350.12921.4511-0.700319.972
101.34780.28410.54620.31130.08790.22430.0181-0.02930.2332-0.0696-0.05080.09030.120.23030.03270.07840.00940.04110.14630.00810.163-9.28441.747814.143
1111.77595.17515.464512.35168.29025.9769-0.7401-2.3715-1.0959-0.23910.25470.447-0.174-0.96790.48540.1641-0.0447-0.01310.16670.05590.15034.3143-17.3378-9.2214
1220.2557-24.90721.81730.6263-26.826823.49862.0849-0.495-1.1843-1.014-0.8061-0.1758-0.695-0.4069-1.27880.33630.0401-0.094-0.1244-0.18970.324811.855-17.0465-13.4893
1315.06931.04312.79614.9723-0.493111.39311.7711-1.32780.8607-1.1965-2.33890.4104-0.1485-0.37970.56780.21760.18250.1348-0.094-0.11130.2384-7.968116.624922.2544
1439.752615.08093.2965.73130.854615.88280.84950.3262-0.07180.6151-1.24480.4267-0.3687-0.15460.39530.04410.02350.0299-0.012-0.11120.2005-4.85617.008529.5166
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA305 - 3439 - 47
2X-RAY DIFFRACTION2AA344 - 40848 - 112
3X-RAY DIFFRACTION3AA409 - 435113 - 139
4X-RAY DIFFRACTION4AA436 - 498140 - 202
5X-RAY DIFFRACTION5AA499 - 549203 - 253
6X-RAY DIFFRACTION6BB306 - 35110 - 55
7X-RAY DIFFRACTION7BB352 - 45856 - 162
8X-RAY DIFFRACTION8BB459 - 476163 - 180
9X-RAY DIFFRACTION9BB477 - 514181 - 218
10X-RAY DIFFRACTION10BB515 - 550219 - 254
11X-RAY DIFFRACTION11CC687 - 6912 - 6
12X-RAY DIFFRACTION12CC692 - 6977 - 12
13X-RAY DIFFRACTION13DD687 - 6912 - 6
14X-RAY DIFFRACTION14DD692 - 6967 - 11

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