[English] 日本語
Yorodumi
- PDB-5tn7: Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tn7
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with (E)-3'-fluoro-4'-hydroxy-3-((hydroxyiminio)methyl)-[1,1'-biphenyl]-4-olate
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / regulation of lipid metabolic process / androgen metabolic process / steroid hormone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / estrogen receptor signaling pathway / cellular response to estrogen stimulus / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / estrogen response element binding / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / : / 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 / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / protein localization to chromatin / 14-3-3 protein binding / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / TBP-class protein binding / nitric-oxide synthase regulator activity / Regulation of lipid metabolism by PPARalpha / steroid binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / BMAL1:CLOCK,NPAS2 activates circadian gene expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / response to progesterone / stem cell differentiation / nuclear receptor binding / nuclear estrogen receptor binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / euchromatin / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / HATs acetylate histones / regulation of inflammatory response / positive regulation of cytosolic calcium ion concentration / fibroblast proliferation / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
Similarity search - Function
Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 receptor coactivator, DUF1518 ...Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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-7G2 / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.238 Å
AuthorsNwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Kojetin, D.J. / Minutolo, F. / Elemento, O. / Katzenellenbogen, J.A. / Nettles, K.W.
CitationJournal: Cell Chem Biol / Year: 2017
Title: Systems Structural Biology Analysis of Ligand Effects on ER alpha Predicts Cellular Response to Environmental Estrogens and Anti-hormone Therapies.
Authors: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Wright, N.J. / Minutolo, F. / Rangarajan, E.S. / Izard, T. / Yao, X.Q. / Grant, B.J. / Kojetin, D.J. / Elemento, O. / ...Authors: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Wright, N.J. / Minutolo, F. / Rangarajan, E.S. / Izard, T. / Yao, X.Q. / Grant, B.J. / Kojetin, D.J. / Elemento, O. / Katzenellenbogen, J.A. / Nettles, K.W.
History
DepositionOct 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 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: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5007
Polymers61,7594
Non-polymers7423
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-29 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.070, 83.400, 58.620
Angle α, β, γ (deg.)90.000, 110.700, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 29299.535 Da / Num. of mol.: 2 / Fragment: ligand-binding domain (UNP residues 298-554) / Mutation: Y537S
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: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1579.866 Da / Num. of mol.: 2
Fragment: Nuclear receptor-interacting peptide (UNP residues 686-698)
Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-7G2 / 3-fluoro-3'-[(E)-(hydroxyimino)methyl][1,1'-biphenyl]-4,4'-diol


Mass: 247.222 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H10FNO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.04 Å3/Da / Density % sol: 39.68 % / Mosaicity: 0.964 °
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 15% PEG 3350, 0.05M MgCl2, 0.067M NaCl, 0.1M Tris

-
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 26, 2013
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: 2.238→50 Å / Num. obs: 23808 / % possible obs: 98.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 33.43 Å2 / Rmerge(I) obs: 0.113 / Net I/av σ(I): 24.581 / Net I/σ(I): 5.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.24-2.285.80.604198
2.28-2.326.10.886199.3
2.32-2.366.50.651199.4
2.36-2.416.60.622199.2
2.41-2.476.90.448199.1
2.47-2.5270.436199
2.52-2.596.90.375198.8
2.59-2.666.80.3198.8
2.66-2.736.60.253198.3
2.73-2.826.10.211195.1
2.82-2.926.90.197199.3
2.92-3.047.20.161199.7
3.04-3.187.10.151199.8
3.18-3.3570.146199.8
3.35-3.566.90.134199.3
3.56-3.836.70.129198.3
3.83-4.225.90.114196
4.22-4.826.80.111199.2
4.82-6.086.80.111199.5
6.08-506.40.069198

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.238→46.67 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.67
RfactorNum. reflection% reflection
Rfree0.2352 1705 8.35 %
Rwork0.1934 --
obs0.1968 20431 85.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.31 Å2 / Biso mean: 53.4304 Å2 / Biso min: 15.48 Å2
Refinement stepCycle: final / Resolution: 2.238→46.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3821 0 52 107 3980
Biso mean--54.74 42.8 -
Num. residues----489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023943
X-RAY DIFFRACTIONf_angle_d0.4625336
X-RAY DIFFRACTIONf_chiral_restr0.032631
X-RAY DIFFRACTIONf_plane_restr0.003662
X-RAY DIFFRACTIONf_dihedral_angle_d13.0632374
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2376-2.30340.2383300.230536539520
2.3034-2.37780.29321200.24371061118160
2.3778-2.46280.2971360.24461549168585
2.4628-2.56140.33011440.22911623176788
2.5614-2.67790.29471520.22731628178090
2.6779-2.81910.25761520.22731675182792
2.8191-2.99570.241610.2231778193997
2.9957-3.22690.25091680.21751792196098
3.2269-3.55160.22641590.19661791195099
3.5516-4.06520.19721560.16741790194696
4.0652-5.12080.2041600.15921822198299
5.1208-46.67990.22211670.17791852201998
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)
16.6944-1.0605-1.85718.34821.36646.45630.51620.78751.1406-0.7301-0.1873-0.0777-0.5822-1.0095-0.13150.53380.2015-0.06940.53790.13950.46020.740718.5971-4.8412
27.33-4.02981.75416.0859-1.06866.131-0.02210.2771-1.2978-0.5873-0.5421-1.04191.59431.02470.21230.78380.17340.30710.64620.12950.836121.3054-6.6729-6.3948
36.04580.2228-1.13623.9878-0.02116.0991-0.1625-0.10020.0398-0.2322-0.0605-0.31760.06720.55010.19150.16180.04050.01790.22760.03560.220716.13897.08182.2286
42.7551.7631-1.73973.60631.42913.565-0.398-0.133-0.90540.38590.2899-0.76841.95950.53980.250.88760.16760.16220.3581-0.01240.620615.3678-11.89891.369
56.1016-0.7595-1.51864.7948-0.87056.3177-0.19680.113-0.363-0.051-0.1057-0.00940.7487-0.07280.26510.22390.02020.07010.1839-0.01140.18815.46622.4186.2577
65.843-0.4145-0.99024.35160.25235.399-0.13870.09370.28130.0995-0.0997-0.00840.049-0.26490.15990.24420.00980.00220.16650.00570.15812.40547.45798.6483
76.85430.473-1.10456.0614-2.94317.0877-0.314-1.3793-0.6750.05650.0162-1.1480.8980.6594-0.0330.36620.1333-0.01550.75790.07660.742428.03763.77529.4925
85.1969-0.97774.77728.2841-1.59256.92430.2932-1.2061-0.8954-0.10340.32271.78250.7408-1.2528-0.31070.4156-0.09790.06820.7563-0.04760.7037-17.44021.511625.9626
92.16940.4521-1.16873.8845-0.53062.4746-0.1451-0.7304-0.19220.44250.2173-1.0534-0.60880.66580.01950.51490.0133-0.05830.708-0.12380.56227.00859.56544.4376
106.5307-0.69681.58094.84131.24493.1812-0.6766-0.1104-0.21820.03080.3428-0.06340.48310.47530.20640.4620.00220.09880.460.04790.23035.32571.16537.8108
114.51920.1144-1.24245.55950.27547.4293-0.1895-0.1371-0.20630.2565-0.05710.21120.58180.09820.23660.23070.0050.02460.22150.03820.15571.17523.073729.7729
123.74720.4665-0.54413.65991.7716.0487-0.0496-0.31350.52120.0580.1699-0.8103-1.32441.3825-0.0710.5294-0.18570.06310.5101-0.10440.446511.601215.769729.4909
134.376-0.56591.10886.4092-2.03167.14790.0680.1104-0.145-0.314-0.27940.48290.5435-1.01370.27670.2502-0.07630.04620.4472-0.08120.2738-8.4473.72719.3013
148.697-1.51422.65414.1778-0.89647.4605-0.2020.0315-0.2660.2633-0.0871-0.153-0.10740.45030.13120.1978-0.01970.06330.1909-0.0320.19425.49597.586620.2052
158.90140.9499-0.83014.5353-2.3356.6901-0.5343-0.8954-0.85340.73670.6157-0.75661.1221.2594-0.08480.82490.33710.04940.72020.09580.69714.7929-5.895635.0746
167.6918-2.90991.45679.5669-4.72389.6083-0.7682-0.06671.26-0.0155-0.6239-1.7236-0.9641.79011.51340.4345-0.15170.03910.5922-0.0510.956624.726217.92311.4008
172.72751.28461.03174.0021-1.73034.9524-0.3665-1.003-1.28350.17960.35060.68621.8374-0.7110.07081.1257-0.2057-0.00520.66930.20220.66410.221-13.152235.3912
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 305 through 321 )A305 - 321
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 338 )A322 - 338
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 397 )A339 - 397
4X-RAY DIFFRACTION4chain 'A' and (resid 398 through 420 )A398 - 420
5X-RAY DIFFRACTION5chain 'A' and (resid 421 through 470 )A421 - 470
6X-RAY DIFFRACTION6chain 'A' and (resid 471 through 530 )A471 - 530
7X-RAY DIFFRACTION7chain 'A' and (resid 531 through 548 )A531 - 548
8X-RAY DIFFRACTION8chain 'B' and (resid 305 through 321 )B305 - 321
9X-RAY DIFFRACTION9chain 'B' and (resid 322 through 338 )B322 - 338
10X-RAY DIFFRACTION10chain 'B' and (resid 339 through 363 )B339 - 363
11X-RAY DIFFRACTION11chain 'B' and (resid 364 through 407 )B364 - 407
12X-RAY DIFFRACTION12chain 'B' and (resid 408 through 438 )B408 - 438
13X-RAY DIFFRACTION13chain 'B' and (resid 439 through 496 )B439 - 496
14X-RAY DIFFRACTION14chain 'B' and (resid 497 through 530 )B497 - 530
15X-RAY DIFFRACTION15chain 'B' and (resid 531 through 547 )B531 - 547
16X-RAY DIFFRACTION16chain 'C' and (resid 688 through 696 )C688 - 696
17X-RAY DIFFRACTION17chain 'D' and (resid 688 through 696 )D688 - 696

+
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://pdbjlvh1.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