[English] 日本語
Yorodumi
- PDB-5tn9: Crystal Structure of the ER-alpha Ligand-binding Domain (L372S,L5... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tn9
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (L372S,L536S) in Complex with the OBHS-BSC, 4-bromophenyl (1R,2R,4S)-5-(4-hydroxyphenyl)-6-(4-(2-(piperidin-1-yl)ethoxy)phenyl)-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonate
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / Nuclear receptor / transcription factor / ligand binding / protein-ligand complex
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of branching involved in prostate gland morphogenesis / prostate epithelial cord elongation / 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 ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of branching involved in prostate gland morphogenesis / prostate epithelial cord elongation / 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 proliferation involved in mammary gland duct elongation / epithelial cell development / vagina development / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / TFIIB-class transcription factor binding / androgen metabolic process / steroid hormone receptor signaling pathway / mammary gland alveolus development / 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 / 14-3-3 protein binding / protein localization to chromatin / estrogen receptor signaling pathway / steroid binding / nitric-oxide synthase regulator activity / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / negative regulation of miRNA transcription / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / SUMOylation of intracellular receptors / euchromatin / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / Constitutive Signaling by Aberrant PI3K in Cancer / male gonad development / nuclear receptor activity / Regulation of RUNX2 expression and activity / positive regulation of fibroblast proliferation / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / regulation of inflammatory response / positive regulation of cytosolic calcium ion concentration / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / fibroblast proliferation / 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 / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / chromatin binding / regulation of DNA-templated transcription / chromatin / 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 / identical protein binding / membrane / 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 ...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-7EC / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.253 Å
AuthorsNwachukwu, J.C. / Sharma, N. / Carlson, K.E. / Srinivasan, S. / Sharma, A. / Katzenellenbogen, J.A. / Nettles, K.W.
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Exploring the Structural Compliancy versus Specificity of the Estrogen Receptor Using Isomeric Three-Dimensional Ligands.
Authors: Sharma, N. / Carlson, K.E. / Nwachukwu, J.C. / Srinivasan, S. / Sharma, A. / Nettles, K.W. / Katzenellenbogen, J.A.
History
DepositionOct 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)119,8008
Polymers117,2944
Non-polymers2,5064
Water5,657314
1
A: Estrogen receptor
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9004
Polymers58,6472
Non-polymers1,2532
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-9 kcal/mol
Surface area18310 Å2
MethodPISA
2
C: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9004
Polymers58,6472
Non-polymers1,2532
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-11 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.430, 58.560, 93.770
Angle α, β, γ (deg.)80.27, 75.04, 62.84
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 29323.469 Da / Num. of mol.: 4 / Fragment: ligand-binding domain / Mutation: L372S, L536S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03372
#2: Chemical
ChemComp-7EC / 4-bromophenyl (1S,2R,4S)-5-(4-hydroxyphenyl)-6-{4-[2-(piperidin-1-yl)ethoxy]phenyl}-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonate


Mass: 626.558 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H32BrNO6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.69 % / Mosaicity: 0.419 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2012
RadiationMonochromator: Side scattering bent cube i-beam single crystal asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.253→50 Å / Num. obs: 42008 / % possible obs: 91.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/av σ(I): 15.086 / Net I/σ(I): 5.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.26-2.33.70.352193.1
2.3-2.343.70.317193.4
2.34-2.393.70.303193
2.39-2.433.70.251191.9
2.43-2.493.80.237192.3
2.49-2.553.70.216192.4
2.55-2.613.80.191191.5
2.61-2.683.80.169190.2
2.68-2.763.80.16187.3
2.76-2.853.80.129178
2.85-2.953.80.111194.4
2.95-3.073.80.097195.5
3.07-3.213.80.085194.3
3.21-3.383.80.075193.7
3.38-3.593.90.065192.7
3.59-3.863.80.061189
3.86-4.253.70.053182.3
4.25-4.873.90.049196
4.87-6.133.90.052193.6
6.13-503.90.038189.4

-
Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.253→46.292 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0.15 / Phase error: 23.97
RfactorNum. reflection% reflection
Rfree0.2381 1867 4.76 %
Rwork0.2068 --
obs0.2083 39190 85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.253→46.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6762 0 135 314 7211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027064
X-RAY DIFFRACTIONf_angle_d0.5649588
X-RAY DIFFRACTIONf_dihedral_angle_d14.6432586
X-RAY DIFFRACTIONf_chiral_restr0.021150
X-RAY DIFFRACTIONf_plane_restr0.0021169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2529-2.31380.2522940.24131759X-RAY DIFFRACTION52
2.3138-2.38180.28371260.24452673X-RAY DIFFRACTION80
2.3818-2.45870.30711450.23592901X-RAY DIFFRACTION86
2.4587-2.54660.28131610.23072974X-RAY DIFFRACTION87
2.5466-2.64850.26061510.22452907X-RAY DIFFRACTION86
2.6485-2.76910.241450.22642800X-RAY DIFFRACTION84
2.7691-2.9150.23021370.21732824X-RAY DIFFRACTION83
2.915-3.09760.2891540.21143154X-RAY DIFFRACTION94
3.0976-3.33680.24041460.21173156X-RAY DIFFRACTION93
3.3368-3.67240.19551610.19613081X-RAY DIFFRACTION91
3.6724-4.20350.18861420.17412828X-RAY DIFFRACTION84
4.2035-5.29480.24421640.18263233X-RAY DIFFRACTION95
5.2948-46.30190.22361410.21313033X-RAY DIFFRACTION90
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)
12.09640.5082-0.17432.99240.55842.0793-0.0757-0.02960.21440.0112-0.00540.11-0.0936-0.10410.12460.16970.0856-0.01170.15140.02210.14598.341922.478742.2951
25.1260.0901-0.14322.93140.15814.1279-0.1620.09780.1577-0.22240.0173-0.21390.08510.14990.07070.11620.0591-0.00060.06130.00860.215412.154713.597235.5723
31.93630.4207-0.74373.6496-0.01482.55440.1033-0.1332-0.00170.3993-0.04640.00350.1708-0.27720.00480.09770.08750.00540.04280.02190.18316.06828.718340.3053
43.2038-0.5861.67092.4423-0.43585.8799-0.10340.3258-0.0869-0.4627-0.0167-0.52150.23520.4358-0.00230.40660.06190.07130.2013-0.0690.224621.7394-14.42533.3752
53.0982-1.37620.52283.6721-0.43811.8958-0.1218-0.03260.17280.10660.0425-0.3250.17570.080.07030.17870.020.0480.1017-0.0010.132918.4377-5.874740.1082
61.3436-0.4847-0.91311.7815-0.52721.7805-0.3164-0.33530.74030.1572-0.7065-0.5041-0.12650.43710.09630.08720.09350.10390.91880.0610.977635.62580.188441.2785
71.7587-0.33960.04564.17170.60052.4597-0.0312-0.044-0.15170.1180.0334-0.00790.1423-0.07340.0030.125-0.0666-0.00280.14520.02490.19039.74095.24586.056
84.2142-1.27393.97160.6716-1.30093.75830.8116-0.3662-0.0513-0.8253-0.08260.16240.6310.2642-0.79961.0638-0.2350.04460.6331-0.12610.60416.015824.922872.0354
91.5999-0.30080.50544.34691.19992.60620.07240.24510.201-0.3265-0.03370.1565-0.1285-0.2158-0.02560.1503-0.0669-0.01270.17960.05750.21666.947516.894685.6854
103.50060.1247-0.16763.5561-0.74131.4037-0.1880.21630.0228-0.17770.171-0.3301-0.30060.3758-0.00330.2161-0.129-0.01580.1407-0.01030.125524.739335.224584.4287
111.49050.618-1.32272.11950.78762.0412-0.03980.0052-0.1378-0.16350.04040.2907-0.1483-0.01730.01510.176-0.0595-0.02250.1707-0.01380.120616.423329.1788.1978
122.98951.15550.76183.3706-0.75053.6399-0.1244-0.1363-0.20110.08860.0192-0.0663-0.3060.1864-0.02170.0834-0.0418-0.00950.0852-0.01090.128917.26527.617391.0447
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 306:411)
2X-RAY DIFFRACTION2(chain A and resid 412:461)
3X-RAY DIFFRACTION3(chain A and resid 468:546)
4X-RAY DIFFRACTION4(chain B and resid 305:342)
5X-RAY DIFFRACTION5(chain B and resid 343:522)
6X-RAY DIFFRACTION6(chain B and resid 523:546)
7X-RAY DIFFRACTION7(chain C and resid 307:458)
8X-RAY DIFFRACTION8(chain C and resid 459:467)
9X-RAY DIFFRACTION9(chain C and resid 468:546)
10X-RAY DIFFRACTION10(chain D and resid 305:425)
11X-RAY DIFFRACTION11(chain D and resid 426:469)
12X-RAY DIFFRACTION12(chain D and resid 470:546)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more