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- PDB-1hcq: THE CRYSTAL STRUCTURE OF THE ESTROGEN RECEPTOR DNA-BINDING DOMAIN... -

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Basic information

Entry
Database: PDB / ID: 1hcq
TitleTHE CRYSTAL STRUCTURE OF THE ESTROGEN RECEPTOR DNA-BINDING DOMAIN BOUND TO DNA: HOW RECEPTORS DISCRIMINATE BETWEEN THEIR RESPONSE ELEMENTS
Components
  • DNA (5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*CP*AP*GP*TP*GP*AP*CP*CP*T P*G)-3')
  • DNA (5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*CP*TP*GP*TP*GP*AP*CP*CP*T P*G)-3')
  • PROTEIN (ESTROGEN RECEPTOR)
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / COMPLEXED WITH DRUG / TRANSCRIPTION-DNA COMPLEX
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 receptor signaling pathway / mammary gland alveolus development / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / : / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / negative regulation of miRNA transcription / protein localization to chromatin / 14-3-3 protein binding / cellular response to estradiol stimulus / transcription coregulator binding / nitric-oxide synthase regulator activity / steroid binding / TBP-class protein binding / ESR-mediated signaling / transcription corepressor binding / positive regulation of nitric-oxide synthase activity / SUMOylation of intracellular receptors / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / euchromatin / negative regulation of DNA-binding transcription factor activity / Constitutive Signaling by Aberrant PI3K in Cancer / transcription coactivator binding / nuclear receptor activity / beta-catenin binding / positive regulation of fibroblast proliferation / response to estrogen / Regulation of RUNX2 expression and activity / male gonad development / PIP3 activates AKT signaling / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / regulation of inflammatory response / response to estradiol / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / fibroblast proliferation / transcription regulator complex / Estrogen-dependent gene expression / 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 / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / protein kinase binding / 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 / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / 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 hormone receptor ...Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / 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 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 / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Ligand-binding domain of nuclear hormone receptor / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsSchwabe, J.W.R. / Chapman, L. / Finch, J.T. / Rhodes, D.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1993
Title: The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements.
Authors: Schwabe, J.W. / Chapman, L. / Finch, J.T. / Rhodes, D.
#1: Journal: Structure / Year: 1993
Title: DNA Recognition by the Oestrogen Receptor: From Solution to the Crystal
Authors: Schwabe, J.W.R. / Chapman, L. / Finch, J.T. / Rhodes, D. / Neuhaus, D.
History
DepositionJan 4, 1995Deposition site: NDB / Processing site: NDB
Revision 1.0Nov 23, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _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
C: DNA (5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*CP*AP*GP*TP*GP*AP*CP*CP*T P*G)-3')
D: DNA (5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*CP*TP*GP*TP*GP*AP*CP*CP*T P*G)-3')
G: DNA (5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*CP*AP*GP*TP*GP*AP*CP*CP*T P*G)-3')
H: DNA (5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*CP*TP*GP*TP*GP*AP*CP*CP*T P*G)-3')
A: PROTEIN (ESTROGEN RECEPTOR)
B: PROTEIN (ESTROGEN RECEPTOR)
E: PROTEIN (ESTROGEN RECEPTOR)
F: PROTEIN (ESTROGEN RECEPTOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,35716
Polymers60,8338
Non-polymers5238
Water2,846158
1
C: DNA (5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*CP*AP*GP*TP*GP*AP*CP*CP*T P*G)-3')
D: DNA (5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*CP*TP*GP*TP*GP*AP*CP*CP*T P*G)-3')
A: PROTEIN (ESTROGEN RECEPTOR)
B: PROTEIN (ESTROGEN RECEPTOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6788
Polymers30,4174
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: DNA (5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*CP*AP*GP*TP*GP*AP*CP*CP*T P*G)-3')
H: DNA (5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*CP*TP*GP*TP*GP*AP*CP*CP*T P*G)-3')
E: PROTEIN (ESTROGEN RECEPTOR)
F: PROTEIN (ESTROGEN RECEPTOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6788
Polymers30,4174
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.600, 90.800, 114.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*CP*AP*GP*TP*GP*AP*CP*CP*T P*G)-3')


Mass: 5501.568 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*CP*AP*GP*GP*TP*CP*AP*CP*TP*GP*TP*GP*AP*CP*CP*T P*G)-3')


Mass: 5492.554 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein
PROTEIN (ESTROGEN RECEPTOR)


Mass: 9711.269 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P03372
#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.: 158 / 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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal grow
*PLUS
Temperature: 8 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.07 mMDNA duplex1drop
20.14 mM440-5251drop
31.8 mM1dropMgSO4
425 mM1dropNaCl
61.8 mMspermine1drop
70.002 mM1dropZnCl2
80.2 M1reservoirNaCl
5MES1drop
9MES1reservoir
108 %methyl pentane1reservoiror ethanol

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Num. obs: 20360 / % possible obs: 93.9 % / Num. measured all: 98492 / Rmerge(I) obs: 0.107
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.53 Å / % possible obs: 87.3 % / Rmerge(I) obs: 0.402

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Processing

Software
NameClassification
X-PLORrefinement
TNTrefinement
RefinementRfactor Rwork: 0.204 / Rfactor obs: 0.204 / Highest resolution: 2.4 Å
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2240 1458 8 158 3864
Software
*PLUS
Name: X-PLOR/TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_angle_deg2.55

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