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- PDB-2jf9: ESTROGEN RECEPTOR ALPHA LBD IN COMPLEX WITH A TAMOXIFEN-SPECIFIC ... -

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Basic information

Entry
Database: PDB / ID: 2jf9
TitleESTROGEN RECEPTOR ALPHA LBD IN COMPLEX WITH A TAMOXIFEN-SPECIFIC PEPTIDE ANTAGONIST
Components
  • AB5 PEPTIDE
  • ESTROGEN RECEPTOR
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR / LIPID-BINDING / TRANSCRIPTION REGULATION / LIGAND-BINDING DOMAIN (LBD) / RECEPTOR / ZINC-FINGER / DNA-BINDING / STEROID-BINDING / NUCLEAR RECEPTOR / PEPTIDE ANTAGONIST / METAL-BINDING / NUCLEAR PROTEIN / PHOSPHORYLATION
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / 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 ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / 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 / mammary gland branching involved in pregnancy / uterus development / negative regulation of smooth muscle cell apoptotic process / vagina development / TFIIB-class transcription factor binding / androgen 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 / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / protein localization to chromatin / steroid binding / 14-3-3 protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / negative regulation of canonical NF-kappaB signal transduction / ESR-mediated signaling / negative regulation of miRNA transcription / TBP-class protein binding / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / transcription corepressor binding / transcription coregulator binding / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / transcription coactivator binding / male gonad development / nuclear receptor activity / positive regulation of fibroblast proliferation / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / response to estradiol / PIP3 activates AKT signaling / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / calmodulin binding / Extra-nuclear estrogen signaling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor ...Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / 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 / 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
BICARBONATE ION / 4-HYDROXYTAMOXIFEN / Estrogen receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHeldring, N. / Pawson, T. / McDonnell, D. / Treuter, E. / Gustafsson, J.A. / Pike, A.C.W.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural Insights Into Corepressor Recognition by Antagonist-Bound Estrogen Receptors.
Authors: Heldring, N. / Pawson, T. / Mcdonnell, D. / Treuter, E. / Gustafsson, J.A. / Pike, A.C.W.
History
DepositionJan 29, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 21, 2016Group: Source and taxonomy / Structure summary
Revision 1.3Jan 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 1.4Dec 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: ESTROGEN RECEPTOR
P: AB5 PEPTIDE
Q: AB5 PEPTIDE
R: AB5 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,31918
Polymers90,6436
Non-polymers1,67612
Water5,332296
1
A: ESTROGEN RECEPTOR
B: ESTROGEN RECEPTOR
C: ESTROGEN RECEPTOR
P: AB5 PEPTIDE
Q: AB5 PEPTIDE
R: AB5 PEPTIDE
hetero molecules

A: ESTROGEN RECEPTOR
B: ESTROGEN RECEPTOR
C: ESTROGEN RECEPTOR
P: AB5 PEPTIDE
Q: AB5 PEPTIDE
R: AB5 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,63836
Polymers181,28612
Non-polymers3,35224
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)193.707, 193.707, 64.441
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-2092-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.132, 0.767, -0.628), (0.764, -0.482, -0.429), (-0.631, -0.423, -0.65)60.20348, -13.82353, 91.19273
2given(-0.152, 0.95, -0.274), (0.946, 0.059, -0.32), (-0.287, -0.307, -0.907)27.10186, -10.80612, 46.9469
3given(0.004, 0.751, -0.661), (0.736, -0.449, -0.506), (-0.677, -0.484, -0.554)69.58496, -13.06248, 95.84724
4given(-0.158, 0.948, -0.278), (0.946, 0.065, -0.318), (-0.283, -0.313, -0.907)27.91552, -11.17572, 46.88354

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Components

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Protein / Protein/peptide , 2 types, 6 molecules ABCPQR

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


Mass: 28672.541 Da / Num. of mol.: 3 / Fragment: LIGAND-BINDING DOMAIN, RESIDUES 304-533
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/peptide AB5 PEPTIDE


Mass: 1541.728 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: PEPTIDE DERIVED FROM PHAGE DISPLAY SCREEN OF RANDOM PEPTIDE LIBRARY
Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 5 types, 308 molecules

#3: Chemical ChemComp-OHT / 4-HYDROXYTAMOXIFEN


Mass: 387.514 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H29NO2
#4: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 4.08 Å3/Da / Density % sol: 70 %
Crystal growpH: 8.5
Details: 2.5% PEG550MME 2.5% PEK20K 0.06M CALCIUM ACETATE 0.1M TRIS PH8.5, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 80788 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BJ4

2bj4


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.324 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 4054 5 %RANDOM
Rwork0.18 ---
obs0.181 76697 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.07 Å20 Å2
2---0.15 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5315 0 117 296 5728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215574
X-RAY DIFFRACTIONr_bond_other_d0.0010.023725
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.9917507
X-RAY DIFFRACTIONr_angle_other_deg1.7173.0029065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.985667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98223.947228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.902151024
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6741531
X-RAY DIFFRACTIONr_chiral_restr0.0770.2860
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025974
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021036
X-RAY DIFFRACTIONr_nbd_refined0.2120.21228
X-RAY DIFFRACTIONr_nbd_other0.1740.23707
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22690
X-RAY DIFFRACTIONr_nbtor_other0.0870.22654
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2237
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.811.53488
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.31225415
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.89232368
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8954.52092
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.221 284
Rwork0.192 5663
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)
13.5548-0.649-0.13621.6063-0.1851.08860.05770.0587-0.0329-0.1644-0.03580.20420.011-0.0933-0.0218-0.09690.0277-0.0152-0.18260.0051-0.102776.87539.245110.2447
21.21150.10340.24972.9097-1.12511.87390.0313-0.0417-0.03950.08090.02340.05560.144-0.0354-0.0547-0.07830.03170.0012-0.18450.0004-0.175894.327622.534919.3205
31.5082-0.79270.10882.3575-0.43291.2188-0.0058-0.1339-0.3924-0.02880.03890.22190.1472-0.0307-0.0331-0.18140.06960.0151-0.04170.0323-0.085250.040761.15233.6085
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A305 - 528
2X-RAY DIFFRACTION1P1 - 13
3X-RAY DIFFRACTION2B306 - 529
4X-RAY DIFFRACTION2Q1 - 13
5X-RAY DIFFRACTION3C305 - 529
6X-RAY DIFFRACTION3R1 - 13

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