[English] 日本語
Yorodumi
- PDB-3uud: Crystal structure of hERa-LBD (Y537S) in complex with estradiol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uud
TitleCrystal structure of hERa-LBD (Y537S) in complex with estradiol
Components
  • (Estrogen receptor) x 2
  • Nuclear receptor coactivator 1
KeywordsHORMONE RECEPTOR / Ligand-binding domain of nuclear hormone receptor
Function / homology
Function and homology information


labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / RUNX1 regulates transcription of genes involved in WNT signaling ...labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / 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 / hypothalamus development / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / male mating behavior / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / epithelial cell development / negative regulation of smooth muscle cell apoptotic process / uterus development / mammary gland branching involved in pregnancy / vagina development / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / steroid hormone receptor signaling pathway / androgen metabolic process / Synthesis of bile acids and bile salts / cellular response to estrogen stimulus / mammary gland alveolus development / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Mitochondrial unfolded protein response (UPRmt) / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / nuclear retinoid X receptor binding / response to retinoic acid / progesterone receptor signaling pathway / Nuclear signaling by ERBB4 / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to hormone stimulus / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / Recycling of bile acids and salts / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / estrous cycle / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / protein localization to chromatin / estrogen receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / positive regulation of adipose tissue development / steroid binding / : / 14-3-3 protein binding / lactation / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / peroxisome proliferator activated receptor signaling pathway / TBP-class protein binding / regulation of cellular response to insulin stimulus / nitric-oxide synthase regulator activity / positive regulation of nitric-oxide synthase activity / positive regulation of neuron differentiation / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / ESR-mediated signaling / positive regulation of DNA-binding transcription factor activity / hippocampus development / transcription coregulator binding / response to progesterone / transcription corepressor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor binding / negative regulation of DNA-binding transcription factor activity / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / mRNA transcription by RNA polymerase II / Heme signaling
Similarity search - Function
Nuclear receptor coactivator 1 / 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 1 / 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 / Nuclear receptor coactivators bHLH domain / : / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ESTRADIOL / Estrogen receptor / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDelfosse, V. / Grimaldi, M. / Bourguet, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural and mechanistic insights into bisphenols action provide guidelines for risk assessment and discovery of bisphenol A substitutes.
Authors: Delfosse, V. / Grimaldi, M. / Pons, J.L. / Boulahtouf, A. / le Maire, A. / Cavailles, V. / Labesse, G. / Bourguet, W. / Balaguer, P.
History
DepositionNov 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
C: Nuclear receptor coactivator 1
D: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,38010
Polymers60,4974
Non-polymers8836
Water6,810378
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-31 kcal/mol
Surface area20350 Å2
MethodPISA
2
A: Estrogen receptor
C: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6134
Polymers30,2492
Non-polymers3642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-10 kcal/mol
Surface area11770 Å2
MethodPISA
3
B: Estrogen receptor
D: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7676
Polymers30,2492
Non-polymers5194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-9 kcal/mol
Surface area11760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.230, 82.010, 58.930
Angle α, β, γ (deg.)90.00, 111.06, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 2 molecules AB

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


Mass: 28656.742 Da / Num. of mol.: 1 / Fragment: Ligand binding domain (residues 302-552) / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03372
#2: Protein Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 28656.742 Da / Num. of mol.: 1 / Fragment: Ligand binding domain (residues 302-552) / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03372

-
Protein/peptide , 1 types, 2 molecules CD

#3: Protein/peptide Nuclear receptor coactivator 1 / NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal ...NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal carcinoma antigen NY-REN-52 / Steroid receptor coactivator 1 / SRC-1


Mass: 1591.880 Da / Num. of mol.: 2 / Fragment: Coactivator peptide SRC-1 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase

-
Non-polymers , 4 types, 384 molecules

#4: Chemical ChemComp-EST / ESTRADIOL


Mass: 272.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24O2 / Comment: hormone*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200 mM Li2SO4, 100 mM Tris pH 8.5, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 23, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.6→45.7 Å / Num. all: 65563 / Num. obs: 65563 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 19.43 Å2 / Rsym value: 0.039 / Net I/σ(I): 18.19
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.53 / Num. unique all: 9907 / Rsym value: 0.47 / % possible all: 99.8

-
Processing

Software
NameClassification
MxCuBEdata collection
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L03

3l03


Resolution: 1.6→45.675 Å / SU ML: 0.19 / σ(F): 2 / Phase error: 19.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1948 3278 5 %Random
Rwork0.1658 ---
obs0.1672 65563 99.66 %-
all-65563 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.048 Å2 / ksol: 0.381 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7476 Å2-0 Å20.8555 Å2
2--0.2271 Å20 Å2
3----1.9747 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3914 0 62 378 4354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084179
X-RAY DIFFRACTIONf_angle_d1.0215689
X-RAY DIFFRACTIONf_dihedral_angle_d17.7741582
X-RAY DIFFRACTIONf_chiral_restr0.07679
X-RAY DIFFRACTIONf_plane_restr0.004701
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.6-1.62390.23381420.237726932693100
1.6239-1.64930.24721410.23626942694100
1.6493-1.67630.29981450.236227522752100
1.6763-1.70520.25321400.229326582658100
1.7052-1.73620.27021430.229227072707100
1.7362-1.76960.29481430.208527232723100
1.7696-1.80570.22311420.197727022702100
1.8057-1.8450.21411420.188626832683100
1.845-1.88790.24921410.176726952695100
1.8879-1.93510.21461430.169527142714100
1.9351-1.98750.19351430.167827032703100
1.9875-2.04590.1981420.166327052705100
2.0459-2.1120.19051430.161327262726100
2.112-2.18750.20091420.157126952695100
2.1875-2.2750.18431440.156527252725100
2.275-2.37860.17291430.154827172717100
2.3786-2.5040.20251420.161127042704100
2.504-2.66080.20851430.166627102710100
2.6608-2.86620.20641430.165827122712100
2.8662-3.15460.19221430.160427262726100
3.1546-3.61090.16011430.150827212721100
3.6109-4.54880.16051440.133427332733100
4.5488-45.69360.19341410.17582687268796
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)
10.6734-0.1312-0.37630.2228-0.00021.3833-0.1332-0.1399-0.03850.10540.04450.00480.0750.0880.08210.10440.00150.02860.0446-0.00260.00812.23242.4996.1616
20.25320.0385-0.39220.02840.03281.7619-0.00610.0226-0.0003-0.0446-0.018-0.0107-0.0475-0.06770.01830.1101-0.00090.0320.0316-0.01480.034312.99126.0899-5.9686
30.0026-0.0265-0.03340.91061.14551.4441-0.2366-0.0505-0.2171-0.25530.2063-0.0901-0.2010.30740.04690.26320.03490.08580.2290.08130.139924.0342-8.09985.8545
40.9623-0.1201-0.49780.06420.2470.7964-0.09210.15760.2078-0.1546-0.04720.0645-0.09440.04350.02730.0890.02850.10180.0309-0.0097-0.097425.27813.7417-28.661
51.0378-0.1671-0.67930.14910.2010.8848-0.02040.0409-0.0389-0.0298-0.02810.00670.0622-0.10070.04510.12130.01110.02060.0294-0.0028-0.000716.42711.7004-20.2402
60.341-0.74750.38242.6053-0.29320.73550.1073-0.05260.1197-0.0921-0.2036-0.4728-0.02130.08840.10190.14420.00840.04820.16240.04760.205638.50073.5642-19.4503
71.85641.5015-1.40682.2765-2.20822.1438-0.45-0.1602-0.558-0.76640.0745-0.36240.6024-0.00750.37730.29360.03030.13170.09320.09350.226711.2359-14.71647.945
80.9040.4461-0.39260.77940.42560.85610.1316-0.05050.2754-0.1454-0.0793-0.0789-0.10520.1162-0.0580.1881-0.0580.16680.11830.00530.252837.647916.336-25.7015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 305:410
2X-RAY DIFFRACTION2chain A and resseq 411:532
3X-RAY DIFFRACTION3chain A and resseq 533:548
4X-RAY DIFFRACTION4chain B and resseq 305:410
5X-RAY DIFFRACTION5chain B and resseq 411:532
6X-RAY DIFFRACTION6chain B and resseq 533:548
7X-RAY DIFFRACTION7chain C
8X-RAY DIFFRACTION8chain D

+
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