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- PDB-3k6p: Estrogen Related Receptor alpha in Complex with an Ether Based Ligand -

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Basic information

Entry
Database: PDB / ID: 3k6p
TitleEstrogen Related Receptor alpha in Complex with an Ether Based Ligand
ComponentsSteroid hormone receptor ERR1
KeywordsHORMONE RECEPTOR / Estrogen related receptor alpha / DNA-binding / Isopeptide bond / Metal-binding / Nucleus / Phosphoprotein / Receptor / Transcription / Transcription regulation / Zinc-finger
Function / homology
Function and homology information


nuclear steroid receptor activity / intercellular bridge / estrogen response element binding / intracellular steroid hormone receptor signaling pathway / steroid binding / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / fibrillar center / Nuclear Receptor transcription pathway / Regulation of RUNX2 expression and activity ...nuclear steroid receptor activity / intercellular bridge / estrogen response element binding / intracellular steroid hormone receptor signaling pathway / steroid binding / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / fibrillar center / Nuclear Receptor transcription pathway / Regulation of RUNX2 expression and activity / nuclear receptor activity / microtubule cytoskeleton / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / protein domain specific binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Oestrogen-related receptor / 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 ...Oestrogen-related receptor / 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-5FB / Steroid hormone receptor ERR1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.996 Å
AuthorsAbad, M.C. / Patch, R.J.
CitationJournal: To be Published
Title: Development of Diaryl Ether based ligands for Estrogen Related Receptor alpha as Potential Anti-Diabetic Agents.
Authors: Patch, R.J. / Searle, L.L. / Kim, A.J. / De, D. / Zhu, X. / Askari, H.B. / O'Neill, J.C. / Abad, M.C. / Rentzeperis, D. / Geisler, J.G.
History
DepositionOct 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 6, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Steroid hormone receptor ERR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5872
Polymers27,1641
Non-polymers4221
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Steroid hormone receptor ERR1
hetero molecules

A: Steroid hormone receptor ERR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1734
Polymers54,3292
Non-polymers8452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area2690 Å2
ΔGint-5 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.007, 103.007, 110.017
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Steroid hormone receptor ERR1 / Estrogen-related receptor / alpha / ERR-alpha / Estrogen receptor-like 1 / Nuclear receptor ...Estrogen-related receptor / alpha / ERR-alpha / Estrogen receptor-like 1 / Nuclear receptor subfamily 3 group B member 1


Mass: 27164.357 Da / Num. of mol.: 1 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERR1, ESRL1, ESRRA, NR3B1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11474
#2: Chemical ChemComp-5FB / 4-(4-{[(5R)-2,4-dioxo-1,3-thiazolidin-5-yl]methyl}-2-methoxyphenoxy)-3-(trifluoromethyl)benzonitrile


Mass: 422.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H13F3N2O4S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 3.22 Å3/Da / Density % sol: 61.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium Sulfate, PIPES and Sodium Thiocyanate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: May 4, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.996→69 Å / Num. obs: 23992 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 11.87 % / Biso Wilson estimate: 13.77 Å2 / Rmerge(I) obs: 0.374 / Rsym value: 0.1008 / Net I/σ(I): 8.2
Reflection shellResolution: 1.996→2.07 Å / Redundancy: 11.87 % / Mean I/σ(I) obs: 2.18 / Rsym value: 0.4467 / % possible all: 99.92

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
CNSrefinement
PROTEUM PLUSPLUSdata collection
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XB7

1xb7


Resolution: 1.996→51.504 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.88 / Isotropic thermal model: anisotropic / σ(F): 0.18 / Phase error: 20.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 2000 8.35 %
Rwork0.2108 --
obs0.2139 23965 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.205 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso mean: 18.033 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å20 Å20 Å2
2---1.73 Å2-0 Å2
3---3.461 Å2
Refinement stepCycle: LAST / Resolution: 1.996→51.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 29 127 1908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081808
X-RAY DIFFRACTIONf_angle_d1.1092447
X-RAY DIFFRACTIONf_dihedral_angle_d16.934682
X-RAY DIFFRACTIONf_chiral_restr0.065287
X-RAY DIFFRACTIONf_plane_restr0.007307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.996-2.04590.32481370.29891504X-RAY DIFFRACTION99
2.0459-2.10120.32831410.28851550X-RAY DIFFRACTION100
2.1012-2.1630.30551390.26211530X-RAY DIFFRACTION100
2.163-2.23280.27511400.23511543X-RAY DIFFRACTION100
2.2328-2.31260.28671410.2021540X-RAY DIFFRACTION100
2.3126-2.40520.24231410.20041539X-RAY DIFFRACTION100
2.4052-2.51470.21611410.19121556X-RAY DIFFRACTION100
2.5147-2.64730.23091410.19021553X-RAY DIFFRACTION100
2.6473-2.81310.26281400.19451545X-RAY DIFFRACTION100
2.8131-3.03030.2161450.19531582X-RAY DIFFRACTION100
3.0303-3.33520.24221440.20821581X-RAY DIFFRACTION100
3.3352-3.81770.21121450.18431592X-RAY DIFFRACTION100
3.8177-4.80930.19581460.17141611X-RAY DIFFRACTION100
4.8093-51.52060.23621590.2021739X-RAY DIFFRACTION100

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