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- PDB-2bj4: ESTROGEN RECEPTOR ALPHA LBD IN COMPLEX WITH A PHAGE-DISPLAY DERIV... -

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Basic information

Entry
Database: PDB / ID: 2bj4
TitleESTROGEN RECEPTOR ALPHA LBD IN COMPLEX WITH A PHAGE-DISPLAY DERIVED PEPTIDE ANTAGONIST
Components
  • (ESTROGEN RECEPTOR) x 2
  • PEPTIDE ANTAGONIST
KeywordsNUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / PEPTIDE ANTAGONIST / LIGAND-BINDING DOMAIN (LBD) / DNA-BINDING / NUCLEAR PROTEIN STEROID-BINDING
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 / 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 ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / 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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / prostate epithelial cord elongation / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / steroid hormone mediated signaling pathway / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / : / intracellular steroid hormone receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / 14-3-3 protein binding / TBP-class protein binding / steroid binding / nitric-oxide synthase regulator activity / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / negative regulation of miRNA transcription / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of nitric-oxide synthase activity / SUMOylation of intracellular receptors / euchromatin / negative regulation of DNA-binding transcription factor activity / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / response to estrogen / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / positive regulation of nitric oxide biosynthetic process / male gonad development / positive regulation of fibroblast proliferation / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / fibroblast proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / Extra-nuclear estrogen signaling / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. ...Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / 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
4-HYDROXYTAMOXIFEN / Estrogen receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKong, E. / Heldring, N. / Gustafsson, J.A. / Treuter, E. / Hubbard, R.E. / Pike, A.C.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Delineation of a Unique Protein-Protein Interaction Site on the Surface of the Estrogen Receptor
Authors: Kong, E. / Heldring, N. / Gustafsson, J.A. / Treuter, E. / Hubbard, R.E. / Pike, A.C.W.
History
DepositionJan 28, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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: PEPTIDE ANTAGONIST
D: PEPTIDE ANTAGONIST
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7856
Polymers60,0104
Non-polymers7752
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-37.6 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.760, 98.760, 105.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.97651, -0.2018, 0.07552), (-0.21237, 0.96061, -0.17926), (-0.03637, -0.19109, -0.9809)26.17764, 6.96425, 45.18856
2given(-0.97513, -0.20806, 0.07633), (-0.21901, 0.95737, -0.18837), (-0.03388, -0.2004, -0.97913)26.42859, 7.67486, 45.78958

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Components

#1: Protein ESTROGEN RECEPTOR / / ER / ESTRADIOL RECEPTOR / ER-ALPHA


Mass: 28672.541 Da / Num. of mol.: 1 / Fragment: RESIDUES 305-533 (LIGAND-BINDING DOMAIN)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET15B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P03372
#2: Protein ESTROGEN RECEPTOR / / ER / ESTRADIOL RECEPTOR / ER-ALPHA


Mass: 28730.576 Da / Num. of mol.: 1 / Fragment: RESIDUES 305-533 (LIGAND-BINDING DOMAIN)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET15B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P03372
#3: Protein/peptide PEPTIDE ANTAGONIST


Mass: 1303.401 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Chemical ChemComp-OHT / 4-HYDROXYTAMOXIFEN / Afimoxifene


Mass: 387.514 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H29NO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: NUCLEAR HORMONE RECEPTOR
Sequence detailsN-TERMINAL HIS-TAG LBD TRUNCATED AT END OF H11

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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: 2.41 Å3/Da / Density % sol: 48.59 %
Crystal growpH: 8
Details: 20% PEG2000MME 0.6M SODIUM FORMATE 0.1M TRIS PH8, PH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 34714 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3 / % possible all: 78.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ERE

1ere


Resolution: 2→28.99 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1725 5 %RANDOM
Rwork0.187 ---
obs0.189 32933 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3649 0 58 179 3886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213817
X-RAY DIFFRACTIONr_bond_other_d0.0020.023595
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.9755156
X-RAY DIFFRACTIONr_angle_other_deg0.8383.0028256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3665455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00324.037161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75915691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7961520
X-RAY DIFFRACTIONr_chiral_restr0.0870.2597
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024108
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02722
X-RAY DIFFRACTIONr_nbd_refined0.2170.2918
X-RAY DIFFRACTIONr_nbd_other0.170.23493
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.22194
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2197
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9651.52507
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35823699
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.16231652
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1634.51457
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.219 85
Rwork0.196 1905
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)
11.5623-0.53860.62032.564-0.84562.48870.014-0.0358-0.0557-0.0573-0.0426-0.07410.05180.12450.0286-0.1419-0.02650.026-0.1259-0.0223-0.147115.685948.486228.9369
21.31790.16340.15582.91310.33222.7056-0.0330.0779-0.0543-0.0463-0.01910.17140.11120.01470.0522-0.1361-0.01010.0019-0.1205-0.0019-0.13462.519644.41426.8058
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A305 - 528
2X-RAY DIFFRACTION1C1 - 11
3X-RAY DIFFRACTION2B304 - 529
4X-RAY DIFFRACTION2D1 - 11

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