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- PDB-2q6j: Crystal Structure of Estrogen Receptor alpha Complexed to a B-N S... -

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Basic information

Entry
Database: PDB / ID: 2q6j
TitleCrystal Structure of Estrogen Receptor alpha Complexed to a B-N Substituted Ligand
Components
  • Estrogen receptor
  • GRIP peptide
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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / locomotor rhythm / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / 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 / transcription regulator inhibitor activity / RNA polymerase II preinitiation complex assembly / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / protein localization to chromatin / positive regulation of adipose tissue development / steroid binding / 14-3-3 protein binding / peroxisome proliferator activated receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / regulation of cellular response to insulin stimulus / negative regulation of miRNA transcription / response to progesterone / ESR-mediated signaling / TBP-class protein binding / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / nuclear receptor binding / transcription coregulator binding / transcription corepressor binding / negative regulation of smoothened signaling pathway / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / mRNA transcription by RNA polymerase II / circadian regulation of gene expression / euchromatin / circadian rhythm / beta-catenin binding / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / 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 / regulation of gene expression / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / calmodulin binding / transcription coactivator activity
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
Chem-A48 / 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: 2.7 Å
AuthorsZhou, H. / Nettles, K.W. / Bruning, J.B. / Kim, Y. / Joachimiak, A. / Sharma, S. / Carlson, K.E. / Stossi, F. / Katzenellenbogen, B.S. / Greene, G.L. / Katzenellenbogen, J.A.
CitationJournal: Chem.Biol. / Year: 2007
Title: Elemental isomerism: a boron-nitrogen surrogate for a carbon-carbon double bond increases the chemical diversity of estrogen receptor ligands
Authors: Zhou, H.-B. / Nettles, K.W. / Bruning, J.B. / Kim, Y. / Joachimiak, A. / Sharma, S. / Carlson, K.E. / Stossi, F. / Katzenellenbogen, B.S. / Greene, G.L. / Katzenellenbogen, J.A.
History
DepositionJun 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 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 1.4Oct 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 1.5Aug 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: GRIP peptide
D: GRIP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8126
Polymers61,9334
Non-polymers8792
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-44 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.551, 79.802, 58.328
Angle α, β, γ (deg.)90.000, 109.880, 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: 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 GRIP peptide


Mass: 1579.866 Da / Num. of mol.: 2 / Fragment: residues 696-698
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ncoa2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BN74, UniProt: Q61026*PLUS
#3: Chemical ChemComp-A48 / 4-[(DIMESITYLBORYL)(2,2,2-TRIFLUOROETHYL)AMINO]PHENOL / (N-2,2,2-TRIFLUOROETHYL-P-HYDROXYLANILINO)DIMESITYLBORANE


Mass: 439.321 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H29BF3NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 1.96 Å3/Da / Density % sol: 37.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25-28% (w/v) PEG monomethyl ether 2000, 0.1M Bis Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97934 Å
DetectorType: SBC / Detector: CCD / Date: Nov 8, 2004 / Details: Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.7→12 Å / Num. all: 12940 / Num. obs: 12940 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 61.6 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Χ2: 1.015 / Net I/σ(I): 6.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.27 / Num. unique all: 1126 / Rsym value: 0.401 / Χ2: 1.897 / % possible all: 82.3

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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: 2.7→12 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.874 / SU B: 40.668 / SU ML: 0.4 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.491 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.297 633 5.1 %RANDOM
Rwork0.227 ---
obs0.231 12322 93.97 %-
all-12322 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.983 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å2-0.3 Å2
2--1.24 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.7→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3953 0 64 1 4018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214114
X-RAY DIFFRACTIONr_angle_refined_deg1.3812.0015561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4785489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.37724.012172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.13915792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8951525
X-RAY DIFFRACTIONr_chiral_restr0.0870.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022957
X-RAY DIFFRACTIONr_nbd_refined0.2860.22269
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22805
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2114
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.23
X-RAY DIFFRACTIONr_mcbond_it0.7821.52529
X-RAY DIFFRACTIONr_mcangle_it1.22523990
X-RAY DIFFRACTIONr_scbond_it0.93831766
X-RAY DIFFRACTIONr_scangle_it1.3154.51571
LS refinement shellResolution: 2.7→2.766 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 35 -
Rwork0.286 747 -
obs-782 83.73 %
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)
110.3583-4.3263-3.96592.05992.1432.4543-0.26180.37280.6835-0.21150.326-0.201-0.1752-0.3753-0.06420.38790.03120.01160.08020.0290.26174.7737.2206-4.8879
25.7431-5.31713.01997.527-6.84277.87640.87971.39950.1233-0.4237-1.3638-0.6591-0.72710.54310.4840.6961-0.05960.23920.2389-0.06410.441433.1769-11.6743-2.547
31.0261-1.8885-1.14164.27770.55534.25020.0788-0.19570.1011-0.38740.0179-0.26220.1638-0.2101-0.09680.418-0.00190.04520.09150.01580.312726.2232-0.26120.4658
412.06182.1418-2.58516.52832.50268.89030.2374-0.57990.6434-0.4303-0.3279-0.0054-0.53460.00920.09050.35020.07660.0233-0.07890.01110.299612.919315.24572.377
52.0314-1.93510.14094.8143-0.34290.6371-0.19320.0353-0.30970.25860.13850.04590.1546-0.07070.05460.3704-0.02610.05990.1299-0.03410.305819.3649-8.67955.7204
65.4501-1.2504-0.07312.5251-1.47273.3245-0.0826-0.0664-0.3381-0.0352-0.0240.19420.1876-0.11080.10660.301-0.01540.04330.0162-0.02890.23846.7947-2.51926.1084
75.87380.0374-5.618720.51796.93657.74390.056-2.20050.9154-0.5379-0.4832-0.2098-0.7237-0.75330.42720.42740.03290.00180.1405-0.10790.38436.065221.269213.302
86.56180.52551.1091.6743-0.03080.1962-0.0095-0.0167-0.2371-0.03580.04550.33710.0787-0.1166-0.0360.36680.02630.08950.1596-0.03210.1856-0.7558-0.56868.2786
96.6023-1.06195.22872.63741.49476.35260.0363-0.60320.47080.20640.1517-0.3332-0.16760.4611-0.1880.36290.07650.084-0.0915-0.02420.33731.0054-0.046312.3863
101.62-2.11716.449923.47-0.371228.81580.0364-1.72030.43360.3193-0.47880.2169-0.5630.38780.44240.2630.04280.04180.0188-0.15910.223626.05828.032314.4646
115.29140.91585.62150.20141.27138.04690.0373-0.0675-0.29790.24720.06050.63330.9491-0.2402-0.09780.3832-0.09530.08040.2154-0.04010.2829-8.3726-5.745331.6273
1213.492511.2711-7.16459.4154-5.98493.80440.26350.8592-0.69290.7843-0.271-1.18380.14141.12170.00760.5096-0.16540.00480.0315-0.03160.292317.186512.045747.0251
131.69462.0382.3724.71920.65875.44290.2826-0.1551-0.25740.5865-0.0981-0.43340.10230.1981-0.18450.34330.04880.0190.1053-0.08810.276512.3259-0.092839.7835
1425.6875-7.6401-0.737212.81882.353313.421-0.2959-0.605-1.2075-0.09610.56150.1530.82750.0455-0.26560.5342-0.1112-0.0409-0.07560.02190.23181.4647-15.675130.5043
151.56281.37040.43761.20270.32673.16340.08330.11-0.06740.0428-0.1492-0.1119-0.05650.20460.06580.42140.00810.0117-0.0034-0.00450.24587.8717-0.856330.2412
168.99370.6192-0.05374.2932-1.852113.0844-0.1534-0.23250.569-0.3197-0.0517-0.2396-0.7540.73060.20510.4723-0.0126-0.04070.1257-0.04810.226210.190615.097735.6992
174.01442.54361.59335.00560.62463.1178-0.1851-0.20760.1107-0.11680.1459-0.153-0.27270.05030.03920.38240.01910.09110.1193-0.03020.19886.39396.781226.022
189.44511.6396-1.884836.8431-8.40232.15970.21752.0362-1.7263-1.5415-1.1073-1.01631.00910.24630.88990.5684-0.02860.01920.1819-0.04960.2074-1.2829-16.122118.8623
195.6984-0.14772.45942.1207-0.80743.4180.06340.12580.1755-0.0208-0.12330.03230.15160.06020.05990.48660.00280.05410.1113-0.07220.28790.60482.561519.3105
2012.09757.6535-9.83684.8421-6.22337.9986-0.0973-0.6085-0.3422-0.2291-0.1679-0.6577-1.01850.41430.26530.50810.1694-0.08360.3747-0.0120.385622.7062-4.970435.198
210.5222.80471.680942.98261.37297.51490.6207-0.87550.7543-1.3458-0.0975-0.6032-0.41850.6325-0.52320.3455-0.0430.06990.1090.04140.648824.453617.09520.8256
2225.2733-12.2589-16.173443.1947-14.197223.3938-0.2135-0.4814-2.10940.54930.49790.6325-0.71811.8466-0.28450.5259-0.0077-0.1953-0.00080.07340.298213.9522-17.509837.295
235.2613-0.107225.45430.0022-0.5184123.14972.24070.1993-2.54941.8992-0.56513.92291.3994-3.6707-1.67560.52870.07410.05520.2182-0.00510.76296.784-17.512140.4696
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA306 - 32710 - 31
2X-RAY DIFFRACTION2AA328 - 33932 - 43
3X-RAY DIFFRACTION3AA340 - 35944 - 63
4X-RAY DIFFRACTION4AA360 - 37664 - 80
5X-RAY DIFFRACTION5AA377 - 42881 - 132
6X-RAY DIFFRACTION6AA429 - 460133 - 164
7X-RAY DIFFRACTION7AA463 - 476167 - 180
8X-RAY DIFFRACTION8AA477 - 519181 - 223
9X-RAY DIFFRACTION9AA520 - 541224 - 245
10X-RAY DIFFRACTION10AA542 - 549246 - 253
11X-RAY DIFFRACTION11BB305 - 3279 - 31
12X-RAY DIFFRACTION12BB328 - 33832 - 42
13X-RAY DIFFRACTION13BB339 - 36043 - 64
14X-RAY DIFFRACTION14BB361 - 37565 - 79
15X-RAY DIFFRACTION15BB376 - 39580 - 99
16X-RAY DIFFRACTION16BB396 - 415100 - 119
17X-RAY DIFFRACTION17BB416 - 458120 - 162
18X-RAY DIFFRACTION18BB470 - 479174 - 183
19X-RAY DIFFRACTION19BB480 - 527184 - 231
20X-RAY DIFFRACTION20BB528 - 548232 - 252
21X-RAY DIFFRACTION21CC688 - 6973 - 12
22X-RAY DIFFRACTION22DD687 - 6912 - 6
23X-RAY DIFFRACTION23DD692 - 6967 - 11

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