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- PDB-1xqc: X-ray structure of ERalpha LBD bound to a tetrahydroisoquinoline ... -

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Basic information

Entry
Database: PDB / ID: 1xqc
TitleX-ray structure of ERalpha LBD bound to a tetrahydroisoquinoline SERM ligand at 2.05A resolution
ComponentsEstrogen receptor
KeywordsHORMONE receptor / alpha-helical sandwich / nuclear hormone receptor / ligand binding domain
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 / prostate epithelial cord elongation / epithelial cell development / 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 / Nuclear signaling by ERBB4 / positive regulation of phospholipase C activity / intracellular steroid hormone receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / steroid binding / nitric-oxide synthase regulator activity / ESR-mediated signaling / 14-3-3 protein binding / transcription corepressor binding / negative regulation of miRNA transcription / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / nuclear estrogen receptor binding / transcription coregulator binding / stem cell differentiation / euchromatin / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / male gonad development / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / positive regulation of nitric oxide biosynthetic process / positive regulation of DNA-binding transcription factor activity / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / sequence-specific double-stranded DNA binding / response to estradiol / PIP3 activates AKT signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / positive regulation of cytosolic calcium ion concentration / fibroblast proliferation / regulation of inflammatory response / 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 / negative regulation of transcription by RNA polymerase II / enzyme binding / 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
Chem-AEJ / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsRenaud, J. / Bischoff, S.F. / Buhl, T. / Floersheim, P. / Fournier, B. / Geiser, M. / Halleux, C. / Kallen, J. / Keller, H.J. / Ramage, P.
CitationJournal: J.Med.Chem. / Year: 2005
Title: Selective Estrogen Receptor Modulators with Conformationally Restricted Side Chains. Synthesis and Structure-Activity Relationship of ERalpha-Selective Tetrahydroisoquinoline Ligands
Authors: Renaud, J. / Bischoff, S.F. / Buhl, T. / Floersheim, P. / Fournier, B. / Geiser, M. / Halleux, C. / Kallen, J. / Keller, H.J. / Ramage, P.
History
DepositionOct 12, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
C: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,6468
Polymers115,8884
Non-polymers1,7584
Water6,738374
1
A: Estrogen receptor
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8234
Polymers57,9442
Non-polymers8792
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-38 kcal/mol
Surface area19220 Å2
MethodPISA
2
C: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8234
Polymers57,9442
Non-polymers8792
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-39 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.114, 156.569, 58.962
Angle α, β, γ (deg.)90.00, 90.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Estrogen receptor / / estrogen receptor alpha / ER / Estradiol receptor / ER-alpha


Mass: 28972.021 Da / Num. of mol.: 4 / Fragment: ligand binding domain / Mutation: C381S, C417S, C530S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pXI317 / Production host: Escherichia coli (E. coli) / References: UniProt: P03372
#2: Chemical
ChemComp-AEJ / (1S)-1-{4-[(9AR)-OCTAHYDRO-2H-PYRIDO[1,2-A]PYRAZIN-2-YL]PHENYL}-2-PHENYL-1,2,3,4-TETRAHYDROISOQUINOLIN-6-OL / 1-[4-(OCTAHYDRO-PYRIDO[1,2-A]PYRAZIN-2-YL)-PHENYL]-2-PHENYL-1,2,3,4-TETRAHYDRO-ISOQUINOLIN-6-OL


Mass: 439.592 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H33N3O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG-550ME, sodium chloride, bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONESRF BM1A10.8727
ROTATING ANODEENRAF-NONIUS FR59121.5418
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEAug 30, 2001
MAC Science DIP-20302IMAGE PLATEJul 12, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.87271
21.54181
ReflectionResolution: 2.05→10 Å / Num. all: 59332 / Num. obs: 59332 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 31.9 Å2 / Rsym value: 0.095 / Net I/σ(I): 22.3
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.422 / % possible all: 89.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1UOM

1uom


Resolution: 2.05→10 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.493 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25425 2992 5.1 %RANDOM
Rwork0.21101 ---
all0.2132 55974 --
obs0.2132 55974 95.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.123 Å2
Baniso -1Baniso -2Baniso -3
1-5.99 Å20 Å2-0.47 Å2
2---1.95 Å20 Å2
3----4.05 Å2
Refinement stepCycle: LAST / Resolution: 2.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7112 0 132 374 7618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0217386
X-RAY DIFFRACTIONr_bond_other_d0.0020.027042
X-RAY DIFFRACTIONr_angle_refined_deg1.55429964
X-RAY DIFFRACTIONr_angle_other_deg0.88316350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.025874
X-RAY DIFFRACTIONr_chiral_restr0.0880.21178
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027818
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021394
X-RAY DIFFRACTIONr_nbd_refined0.2190.21929
X-RAY DIFFRACTIONr_nbd_other0.2290.27989
X-RAY DIFFRACTIONr_nbtor_other0.0880.24216
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2318
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.237
X-RAY DIFFRACTIONr_symmetry_vdw_other0.270.2125
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.216
X-RAY DIFFRACTIONr_mcbond_it0.9421.54422
X-RAY DIFFRACTIONr_mcangle_it1.69327100
X-RAY DIFFRACTIONr_scbond_it2.25232964
X-RAY DIFFRACTIONr_scangle_it3.5814.52864
LS refinement shellResolution: 2.05→2.101 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.352 204
Rwork0.324 3768

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