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- PDB-4aa6: The oestrogen receptor recognizes an imperfectly palindromic resp... -

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Basic information

Entry
Database: PDB / ID: 4aa6
TitleThe oestrogen receptor recognizes an imperfectly palindromic response element through an alternative side-chain conformation
Components
  • 5'-D(*CP*TP*AP*AP*GP*TP*CP*AP*CP*AP*GP*TP*GP*AP *CP*CP*TP*G)-3'
  • 5'-D(*TP*CP*AP*GP*GP*TP*CP*AP*CP*TP*GP*TP*GP*AP *CP*TP*TP*A)-3'
  • ESTROGEN RECEPTOR
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION-DNA COMPLEX / ESTROGEN / ESTROGEN RECEPTOR
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 / TBP-class protein binding / negative regulation of miRNA transcription / 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 / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / 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
Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related receptor / : / Nuclear hormone receptor ...Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Estrogen receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.6 Å
AuthorsSchwabe, J.W. / Chapman, L. / Rhodes, D.
CitationJournal: Structure / Year: 1995
Title: The oestrogen receptor recognizes an imperfectly palindromic response element through an alternative side-chain conformation.
Authors: Schwabe, J.W. / Chapman, L. / Rhodes, D.
History
DepositionNov 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Other / Category: citation / pdbx_database_status
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.status_code_sf
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: 5'-D(*CP*TP*AP*AP*GP*TP*CP*AP*CP*AP*GP*TP*GP*AP *CP*CP*TP*G)-3'
D: 5'-D(*TP*CP*AP*GP*GP*TP*CP*AP*CP*TP*GP*TP*GP*AP *CP*TP*TP*A)-3'
E: ESTROGEN RECEPTOR
F: ESTROGEN RECEPTOR
G: 5'-D(*CP*TP*AP*AP*GP*TP*CP*AP*CP*AP*GP*TP*GP*AP *CP*CP*TP*G)-3'
H: 5'-D(*TP*CP*AP*GP*GP*TP*CP*AP*CP*TP*GP*TP*GP*AP *CP*TP*TP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,59616
Polymers55,0738
Non-polymers5238
Water2,414134
1
A: ESTROGEN RECEPTOR
B: ESTROGEN RECEPTOR
C: 5'-D(*CP*TP*AP*AP*GP*TP*CP*AP*CP*AP*GP*TP*GP*AP *CP*CP*TP*G)-3'
D: 5'-D(*TP*CP*AP*GP*GP*TP*CP*AP*CP*TP*GP*TP*GP*AP *CP*TP*TP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7988
Polymers27,5364
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-31.9 kcal/mol
Surface area12220 Å2
MethodPISA
2
E: ESTROGEN RECEPTOR
F: ESTROGEN RECEPTOR
G: 5'-D(*CP*TP*AP*AP*GP*TP*CP*AP*CP*AP*GP*TP*GP*AP *CP*CP*TP*G)-3'
H: 5'-D(*TP*CP*AP*GP*GP*TP*CP*AP*CP*TP*GP*TP*GP*AP *CP*TP*TP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7988
Polymers27,5364
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-32.5 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.677, 113.093, 62.363
Angle α, β, γ (deg.)90.00, 117.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
ESTROGEN RECEPTOR / ER / ER-ALPHA / ESTRADIOL RECEPTOR / NUCLEAR RECEPTOR SUBFAMILY 3 GROUP A MEMBER 1


Mass: 8264.564 Da / Num. of mol.: 4 / Fragment: RESIDUES 182-252
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03372
#2: DNA chain 5'-D(*CP*TP*AP*AP*GP*TP*CP*AP*CP*AP*GP*TP*GP*AP *CP*CP*TP*G)-3'


Mass: 5500.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#3: DNA chain 5'-D(*TP*CP*AP*GP*GP*TP*CP*AP*CP*TP*GP*TP*GP*AP *CP*TP*TP*A)-3'


Mass: 5506.577 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.42 % / Description: NONE
Crystal growDetails: 20 MM MES PH 5.75, 1.8 MM SPERMINE, 2 MICROMOLAR ZINC CHLORIDE, 30 MM SODIUM CHLORIDE, 12 MM CALCIUM CHLORIDE, 10% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→15.8 Å / Num. obs: 22960 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.07

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.6→7 Å / Data cutoff high absF: 0 / Cross valid method: NONE / σ(F): 2
Details: THESE ARE OLD COORDINATES FOR WHICH WE DO NOT HAVE ALL OF THE INFORMATION
RfactorNum. reflection% reflection
Rwork0.222 --
obs0.222 22960 99.5 %
Refinement stepCycle: LAST / Resolution: 2.6→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2127 1460 8 134 3729
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.193
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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