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- PDB-6d0f: Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Com... -

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Basic information

Entry
Database: PDB / ID: 6d0f
TitleEstrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with 3OHTPE and GRIP Peptide
Components
  • Estrogen receptor
  • GRIP Peptide
KeywordsNUCLEAR PROTEIN / Breast Cancer / Estrogen Receptor / Agonist
Function / homology
Function and homology information


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 ...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 / Synthesis of bile acids and bile salts / cellular response to estrogen stimulus / mammary gland alveolus development / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Mitochondrial unfolded protein response (UPRmt) / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / transcription regulator inhibitor activity / Nuclear signaling by ERBB4 / cellular response to hormone stimulus / Recycling of bile acids and salts / 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 / Regulation of lipid metabolism by PPARalpha / 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 / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / 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 smoothened signaling pathway / 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 / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / transcription coactivator binding / euchromatin / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / response to estrogen / nuclear receptor activity / 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 / HATs acetylate histones / ATPase binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / 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 / 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
4,4',4''-[(2R)-butane-1,1,2-triyl]triphenol / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFanning, S.W. / Han, R. / Maximov, P. / Jordan, V.C. / Greene, G.L.
CitationJournal: To Be Published
Title: Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with 3OHTPE and GRIP Peptide
Authors: fanning, s.w.
History
DepositionApr 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)60,1036
Polymers59,4344
Non-polymers6692
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-27 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.007, 82.992, 58.587
Angle α, β, γ (deg.)90.00, 111.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 28440.465 Da / Num. of mol.: 2 / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03372
#2: Protein/peptide GRIP Peptide


Mass: 1276.530 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others) / References: UniProt: Q15596*PLUS
#3: Chemical ChemComp-FYS / 4,4',4''-[(2R)-butane-1,1,2-triyl]triphenol


Mass: 334.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H22O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 25% PEG 3,350, Tris pH 8.0, 200 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 14884 / % possible obs: 93.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.43
Reflection shellResolution: 2.5001→2.6931 Å / Redundancy: 2.5 % / Num. unique all: 1037 / CC1/2: 0.625 / % possible all: 37

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CBZ

6cbz


Resolution: 2.5→43.082 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2414 694 5.01 %
Rwork0.2098 --
obs0.2114 13847 82.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→43.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3351 0 50 63 3464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033471
X-RAY DIFFRACTIONf_angle_d0.7584700
X-RAY DIFFRACTIONf_dihedral_angle_d13.3861210
X-RAY DIFFRACTIONf_chiral_restr0.026580
X-RAY DIFFRACTIONf_plane_restr0.002575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.69310.2646560.25381199X-RAY DIFFRACTION37
2.6931-2.9640.31171010.26082384X-RAY DIFFRACTION75
2.964-3.39280.28111570.23893200X-RAY DIFFRACTION100
3.3928-4.27390.22661910.18453162X-RAY DIFFRACTION100
4.2739-43.08890.21821890.19583208X-RAY DIFFRACTION100
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)
12.15251.2497-0.71033.82371.07383.5276-0.65430.35570.0506-0.80620.214-0.7042-0.00971.09640.21660.46290.02820.1760.50210.10910.38864.36384.590749.0654
24.0013-0.5247-1.62564.5745-0.61983.5955-0.45940.4519-0.5338-0.4064-0.0043-0.19521.4711-0.2515-0.1460.63190.0680.16520.2515-0.03250.2879-4.5642-2.699347.9065
33.4937-0.69470.86352.29581.40512.8508-0.46180.3808-0.5934-1.2296-0.14690.24871.1285-0.13060.13030.6189-0.05440.1703-0.04510.09120.27-6.5719-0.62954.6286
44.78451.13130.70363.76461.66553.34580.18140.87110.6597-0.21490.1412-0.1111-0.5970.049-0.2320.72450.07070.01230.48640.14530.3362-8.580416.039846.5781
51.39270.5458-0.93922.65271.75512.48250.33290.34010.4364-1.1358-0.05061.4951-1.2797-1.462-0.17520.76350.2808-0.13850.95750.20540.557-18.374415.790246.5764
66.05930.1892-0.44113.72430.42526.6319-0.0939-0.36650.3916-0.14370.13660.1193-0.9132-0.1301-0.01310.29880.03810.03290.19580.04510.1838-4.642411.150358.1706
74.0424-0.9138-0.20433.3521-0.18256.6776-0.0267-0.56-0.32860.3404-0.21230.04780.41381.31380.26090.28210.09210.01320.63730.06150.47765.9521.577566.14
84.81291.2932-1.40684.5777-0.06995.14960.0089-0.09190.3085-0.1483-0.00240.1128-0.626-0.0258-0.06390.1406-0.01250.05020.29940.04180.2152-6.91788.350464.5575
91.87060.47510.9021.4848-0.50092.5566-0.11980.2108-0.7740.48270.22280.27140.31060.0054-0.27930.8252-0.31490.10470.722-0.08820.7782-17.0997-7.076850.6265
104.3898-0.1469-0.82323.1541-0.71895.33820.1049-0.4483-0.02530.2997-0.11830.1336-0.2002-0.0117-0.05080.1992-0.05220.02370.2335-0.03010.1802-18.39875.371285.7312
115.57730.3086-1.15974.78470.51936.138-0.1558-0.27060.19480.1667-0.0033-0.2116-0.1062-0.11590.11120.0940.0188-0.00770.1646-0.00520.1571-16.42515.292279.7406
125.09571.1533-1.40595.13640.3365.4125-0.16780.0471-0.544-0.3082-0.2218-0.05950.93410.27230.05960.3605-0.00340.03440.2281-0.00290.2253-11.8458-1.965277.5649
134.6580.079-0.09532.9404-0.48655.63820.1649-0.67460.10950.0446-0.3241-0.28780.09370.52710.0880.1727-0.0502-0.01510.370.03240.1397-5.11385.492874.3406
147.4931.1584-2.38960.2749-0.28151.80230.14211.56670.1353-0.42330.24370.33760.0835-0.9877-0.39680.3152-0.0306-0.0810.8780.00380.6242-30.98325.489773.7419
151.29581.70541.10413.95120.38551.60610.0070.29-1.67380.08270.1111-0.43571.29180.22820.07161.99220.222-0.2020.5612-0.25440.8833-3.8871-14.619647.3579
162.97760.50430.37673.58270.49343.7203-0.30820.00371.3135-0.7672-0.4871.0606-0.2939-2.1150.39590.56770.5580.21230.92750.07830.9985-29.643617.337180.4517
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 310:340 )A310 - 340
2X-RAY DIFFRACTION2( CHAIN A AND RESID 341:371 )A341 - 371
3X-RAY DIFFRACTION3( CHAIN A AND RESID 372:395 )A372 - 395
4X-RAY DIFFRACTION4( CHAIN A AND RESID 396:407 )A396 - 407
5X-RAY DIFFRACTION5( CHAIN A AND RESID 408:421 )A408 - 421
6X-RAY DIFFRACTION6( CHAIN A AND RESID 422:455 )A422 - 455
7X-RAY DIFFRACTION7( CHAIN A AND RESID 456:496 )A456 - 496
8X-RAY DIFFRACTION8( CHAIN A AND RESID 497:525 )A497 - 525
9X-RAY DIFFRACTION9( CHAIN A AND RESID 526:547 )A526 - 547
10X-RAY DIFFRACTION10( CHAIN B AND RESID 307:362 )B307 - 362
11X-RAY DIFFRACTION11( CHAIN B AND RESID 363:405 )B363 - 405
12X-RAY DIFFRACTION12( CHAIN B AND RESID 406:473 )B406 - 473
13X-RAY DIFFRACTION13( CHAIN B AND RESID 474:528 )B474 - 528
14X-RAY DIFFRACTION14( CHAIN B AND RESID 529:547 )B529 - 547
15X-RAY DIFFRACTION15( CHAIN C AND RESID 688:696 )C688 - 696
16X-RAY DIFFRACTION16( CHAIN D AND RESID 687:696 )D687 - 696

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