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- PDB-5krf: Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) i... -

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Basic information

Entry
Database: PDB / ID: 5krf
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with the Dynamic WAY derivative, 1a
Components
  • Estrogen receptor
  • KHKILHRLLQDSSS Peptide
KeywordsTRANSCRIPTION / Nuclear receptor / transcription factor / ligand binding / protein-ligand complex
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / antral ovarian follicle growth / 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 / nuclear estrogen receptor activity / epithelial cell development / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis ...regulation of epithelial cell apoptotic process / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / antral ovarian follicle growth / 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 / nuclear estrogen receptor activity / epithelial cell development / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / locomotor rhythm / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / aryl hydrocarbon receptor binding / vagina development / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / steroid hormone receptor signaling pathway / androgen metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / Nuclear signaling by ERBB4 / cellular response to hormone stimulus / Recycling of bile acids and salts / transcription regulator inhibitor activity / RNA polymerase II preinitiation complex assembly / positive regulation of DNA-binding transcription factor activity / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / positive regulation of adipose tissue development / protein localization to chromatin / : / steroid binding / Regulation of lipid metabolism by PPARalpha / 14-3-3 protein binding / peroxisome proliferator activated receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / regulation of cellular response to insulin stimulus / negative regulation of DNA-binding transcription factor activity / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / response to progesterone / nitric-oxide synthase regulator activity / Activation of gene expression by SREBF (SREBP) / ESR-mediated signaling / TBP-class protein binding / transcription coregulator binding / nuclear estrogen receptor binding / nuclear receptor binding / transcription corepressor binding / negative regulation of smoothened signaling pathway / stem cell differentiation / cellular response to estradiol stimulus / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / circadian regulation of gene expression / Heme signaling / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / euchromatin / Cytoprotection by HMOX1 / beta-catenin binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / response to estrogen / Regulation of RUNX2 expression and activity / transcription coactivator binding / nuclear receptor activity / Ovarian tumor domain proteases / : / positive regulation of fibroblast proliferation / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / response to estradiol / PIP3 activates AKT signaling / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / positive regulation of cytosolic calcium ion concentration / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of inflammatory response
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 / 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
Chem-6WL / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.193 Å
AuthorsNwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Kojetin, D.J. / 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
DepositionJul 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,5496
Polymers61,9334
Non-polymers6172
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-22 kcal/mol
Surface area20910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.361, 80.875, 58.113
Angle α, β, γ (deg.)90.00, 109.53, 90.00
Int Tables number4
Space group name H-MP1211

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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 / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: This sequence occurs naturally in humans / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03372
#2: Protein/peptide KHKILHRLLQDSSS Peptide


Mass: 1666.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q15596*PLUS
#3: Chemical ChemComp-6WL / 4-[1-methyl-7-(trifluoromethyl)indazol-3-yl]benzene-1,3-diol


Mass: 308.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C15H11F3N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.91 % / Mosaicity: 2.257 °
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 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: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 23951 / % possible obs: 98.3 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.161 / Net I/av σ(I): 15.73 / Net I/σ(I): 4.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.245.90.967199.4
2.24-2.2860.868199.8
2.28-2.326.10.755199.8
2.32-2.3760.737199.9
2.37-2.426.20.637199.7
2.42-2.486.10.586199.8
2.48-2.546.10.535199.4
2.54-2.615.90.483199.3
2.61-2.6960.426198.8
2.69-2.775.60.373197.3
2.77-2.875.50.32195
2.87-2.996.20.265199.8
2.99-3.126.20.227199.4
3.12-3.2960.201199.4
3.29-3.495.70.159198.2
3.49-3.765.50.143196.1
3.76-4.144.70.116191.7
4.14-4.745.60.105197.3
4.74-5.9760.096198.8
5.97-505.70.086197.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.193→45.832 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2661 1834 8.28 %
Rwork0.2261 --
obs0.2293 22143 90.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.193→45.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3843 0 44 141 4028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063989
X-RAY DIFFRACTIONf_angle_d0.9565408
X-RAY DIFFRACTIONf_dihedral_angle_d13.5351473
X-RAY DIFFRACTIONf_chiral_restr0.215638
X-RAY DIFFRACTIONf_plane_restr0.002670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1928-2.25210.36271230.30861402X-RAY DIFFRACTION80
2.2521-2.31830.32421360.28731447X-RAY DIFFRACTION84
2.3183-2.39320.3591320.28771472X-RAY DIFFRACTION87
2.3932-2.47870.33781410.27171498X-RAY DIFFRACTION88
2.4787-2.57790.30531350.28191529X-RAY DIFFRACTION90
2.5779-2.69520.32751400.28051566X-RAY DIFFRACTION90
2.6952-2.83730.32911330.28521498X-RAY DIFFRACTION88
2.8373-3.0150.28691420.25031633X-RAY DIFFRACTION94
3.015-3.24780.26281520.24791639X-RAY DIFFRACTION95
3.2478-3.57450.27031480.22771648X-RAY DIFFRACTION96
3.5745-4.09150.20511440.19051570X-RAY DIFFRACTION92
4.0915-5.15370.20931530.18371672X-RAY DIFFRACTION97
5.1537-45.84180.26131550.19321735X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.28552.80892.59086.30265.67775.3168-0.55710.1920.31360.43090.4828-0.5782-0.6499-0.26580.05220.3929-0.015-0.13990.55410.0290.79352.038340.7344-1.3592
25.5595-5.42950.94315.4846-0.50374.30170.31871.39020.5967-1.1831-0.6798-0.5079-0.149-0.43770.04650.4245-0.005-0.03410.43990.04350.40971.792230.2948-7.0275
33.4989-2.04890.91395.8564-0.8621.66320.51930.2354-0.1327-0.6791-0.5908-0.69460.36160.18490.08760.4112-0.03350.01740.68360.07950.410120.90229.0201-6.3876
42.9923-0.4781-0.23081.00660.48781.5544-0.0075-0.01040.1645-0.04520.0626-0.2828-0.16530.2372-0.02170.2567-0.0141-0.02390.30090.00120.306117.498823.2942.082
54.04461.549-2.53941.1090.10393.7204-0.12430.6713-0.6207-0.3609-0.0136-0.01060.7387-0.16590.0760.4881-0.01320.04750.4232-0.07650.414812.18055.8514-2.8215
64.8322-1.81080.49743.55870.07133.8705-0.3614-0.0416-0.250.16520.2034-0.10790.26570.36750.09690.46170.00780.06870.30820.02340.395111.47224.89117.6324
76.70680.65540.05843.86470.76483.14330.1017-0.23970.6095-0.2359-0.08760.0638-0.4073-0.1592-0.02420.26170.01970.01380.3133-0.00630.27430.66827.32084.0908
89.2468-0.06821.55192.0486-0.25952.6170.2383-0.47710.26470.1032-0.2288-0.10110.41290.0283-0.02520.33420.03240.01240.21730.00330.19287.477417.097411.3791
94.49461.393-1.33224.90241.07997.5163-0.3884-0.63510.33431.14880.1641-0.7691.78240.85310.03890.53320.0929-0.08420.48460.01290.551228.898420.04698.7472
103.8921.49061.1782.57460.85762.88830.1987-0.1164-0.02810.3203-0.02540.1858-0.0111-0.2822-0.12980.41370.03940.08230.51920.03330.397-2.23621.457735.8421
111.90030.11080.4782.76171.44493.4849-0.0375-0.2105-0.14790.17780.01250.03280.14120.12150.0450.3291-0.00350.01960.35620.01580.24334.124518.22232.6092
122.22780.9177-1.2093.2142-3.34343.77091.09-0.12910.61740.9051-0.0548-0.7383-1.16360.7254-0.53290.7227-0.1630.04940.6931-0.01311.445619.526631.522532.9483
136.37280.43460.76364.76760.0495.2788-0.51290.02990.7410.160.2377-0.4636-0.96870.62460.04350.4697-0.08220.01160.374-0.02780.27688.752232.171624.8008
143.29730.91910.32434.24970.02363.93570.30440.15360.2716-0.2164-0.31140.0159-0.279-0.6767-0.04880.36160.0438-0.00650.38940.01290.273-4.52623.610123.7298
157.35642.70675.41676.03211.92914.109-0.5943-0.5884-0.58820.472-0.7975-0.33610.89980.04451.08230.9514-0.01820.22641.18580.01590.53070.62583.849915.3954
161.9335-1.34160.37972.6619-0.89032.4501-0.14470.0567-0.12660.07550.07260.2977-0.0676-0.20980.08420.32540.00140.0780.3017-0.03960.2914-0.320821.236718.6741
176.37741.3129-0.1273.4521-0.41983.1878-0.0281-0.2794-0.1273-0.3406-0.1027-0.40.00390.52120.25440.48620.0296-0.04440.49360.0620.555816.07499.32432.6227
185.0061-2.2931-1.74782.22871.56016.51340.17950.02580.4931-0.0926-0.3648-0.946-1.05531.2913-0.09180.4616-0.08590.10620.60580.010.641226.595733.66051.616
196.5506-0.1939-1.07741.52930.37490.5246-0.3349-0.6842-1.21190.12560.10770.30590.2351-0.0230.20120.6246-0.0227-0.10270.53840.04840.52752.71341.669635.3135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 304 through 311 )
2X-RAY DIFFRACTION2chain 'A' and (resid 312 through 321 )
3X-RAY DIFFRACTION3chain 'A' and (resid 322 through 338 )
4X-RAY DIFFRACTION4chain 'A' and (resid 339 through 394 )
5X-RAY DIFFRACTION5chain 'A' and (resid 395 through 411 )
6X-RAY DIFFRACTION6chain 'A' and (resid 412 through 437 )
7X-RAY DIFFRACTION7chain 'A' and (resid 438 through 496 )
8X-RAY DIFFRACTION8chain 'A' and (resid 497 through 531 )
9X-RAY DIFFRACTION9chain 'A' and (resid 532 through 548 )
10X-RAY DIFFRACTION10chain 'B' and (resid 305 through 338 )
11X-RAY DIFFRACTION11chain 'B' and (resid 339 through 410 )
12X-RAY DIFFRACTION12chain 'B' and (resid 411 through 421 )
13X-RAY DIFFRACTION13chain 'B' and (resid 422 through 437 )
14X-RAY DIFFRACTION14chain 'B' and (resid 438 through 455 )
15X-RAY DIFFRACTION15chain 'B' and (resid 456 through 469 )
16X-RAY DIFFRACTION16chain 'B' and (resid 470 through 531 )
17X-RAY DIFFRACTION17chain 'B' and (resid 532 through 549 )
18X-RAY DIFFRACTION18chain 'C' and (resid 687 through 696 )
19X-RAY DIFFRACTION19chain 'D' and (resid 687 through 696 )

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