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- PDB-2jfa: ESTROGEN RECEPTOR ALPHA LBD IN COMPLEX WITH AN AFFINITY-SELECTED ... -

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Basic information

Entry
Database: PDB / ID: 2jfa
TitleESTROGEN RECEPTOR ALPHA LBD IN COMPLEX WITH AN AFFINITY-SELECTED COREPRESSOR PEPTIDE
Components
  • (ESTROGEN RECEPTOR) x 2
  • COREPRESSOR PEPTIDE
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR / PHAGE DISPLAY / METAL-BINDING / COREPRESSOR / LIPID-BINDING / TRANSCRIPTION REGULATION / LIGAND-BINDING DOMAIN (LBD) / NUCLEAR PROTEIN / PHOSPHORYLATION / STEROID- BINDING / RECEPTOR / ZINC-FINGER / DNA-BINDING / NUCLEAR RECEPTOR / PEPTIDE ANTAGONIST
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
RALOXIFENE / Estrogen receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 / 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
P: COREPRESSOR PEPTIDE
Q: COREPRESSOR PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,54110
Polymers61,2094
Non-polymers1,3316
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)126.573, 126.573, 113.429
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12P
22Q

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A306 - 329
2111B306 - 329
1211A343 - 407
2211B343 - 407
1314A408 - 416
2314B408 - 416
1411A417 - 529
2411B417 - 529
1125P1 - 15
2125Q1 - 15

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.741, -0.671, 0.005), (-0.671, -0.741, 0.019), (-0.009, -0.018, -1)8.46374, 20.93542, 4.34764
2given(0.767, -0.642, -0.009), (-0.642, -0.767, -0.021), (0.007, 0.022, -1)8.53135, 24.03974, 2.94325

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 28672.541 Da / Num. of mol.: 1 / 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 ESTROGEN RECEPTOR / / ER / ESTRADIOL RECEPTOR / ER-ALPHA / ESTROGEN RECEPTOR ALPHA


Mass: 28730.576 Da / Num. of mol.: 1 / 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

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Protein/peptide , 1 types, 2 molecules PQ

#3: Protein/peptide COREPRESSOR PEPTIDE


Mass: 1903.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: BT1 PEPTIDE / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 3 types, 92 molecules

#4: Chemical ChemComp-RAL / RALOXIFENE / Raloxifene


Mass: 473.583 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H27NO4S / Comment: medication*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 4.6 Å3/Da / Density % sol: 73.1 %
Crystal growpH: 5.6
Details: 0.35M AMMONIUM SULPHATE, 0.7M LITHIUM SULPHATE, 0.07M TRI-SODIUM CITRATE PH5.6, pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. obs: 34500 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 59.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.4
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2 / % 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: 2.55→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.95 / SU B: 12.1 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1735 5 %RANDOM
Rwork0.193 ---
obs0.194 32733 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.46 Å2
Baniso -1Baniso -2Baniso -3
1-2.73 Å21.36 Å20 Å2
2--2.73 Å20 Å2
3----4.09 Å2
Refinement stepCycle: LAST / Resolution: 2.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3695 0 88 86 3869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213880
X-RAY DIFFRACTIONr_bond_other_d0.0020.022553
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9965245
X-RAY DIFFRACTIONr_angle_other_deg1.86736270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2145469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.70623.974156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09215702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9211521
X-RAY DIFFRACTIONr_chiral_restr0.0820.2610
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024161
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02740
X-RAY DIFFRACTIONr_nbd_refined0.240.2860
X-RAY DIFFRACTIONr_nbd_other0.1860.22504
X-RAY DIFFRACTIONr_nbtor_refined0.1910.21837
X-RAY DIFFRACTIONr_nbtor_other0.090.21935
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.293
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3370.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7141.52431
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22223772
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.09431661
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2644.51473
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2612tight positional0.060.05
12B2612tight positional0.060.05
11A128medium positional0.650.5
12B128medium positional0.650.5
21P76medium positional0.20.5
22Q76medium positional0.20.5
21P69loose positional0.515
22Q69loose positional0.515
11A2612tight thermal0.210.5
12B2612tight thermal0.210.5
11A128medium thermal0.622
12B128medium thermal0.622
21P76medium thermal0.362
22Q76medium thermal0.362
21P69loose thermal0.7110
22Q69loose thermal0.7110
LS refinement shellResolution: 2.55→2.62 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.317 115
Rwork0.276 2409
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)
13.70310.9712-0.85112.6532-0.62574.10960.0646-0.2096-0.05020.1631-0.2071-0.4369-0.25560.58850.1425-0.1812-0.0989-0.0227-0.19740.0664-0.1663-45.570543.13283.3047
21.3728-1.17080.77894.4881-1.76283.12550.06950.1559-0.0392-0.3318-0.2276-0.28750.4430.12980.1581-0.1033-0.08130.0559-0.26060.0139-0.2165-54.259219.18661.1008
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A305 - 529
2X-RAY DIFFRACTION1P1 - 15
3X-RAY DIFFRACTION2B306 - 528
4X-RAY DIFFRACTION2Q1 - 15

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