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- PDB-3plz: Human LRH1 LBD bound to GR470 -

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Basic information

Entry
Database: PDB / ID: 3plz
TitleHuman LRH1 LBD bound to GR470
Components
  • FTZ-F1 related protein
  • Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION/RECEPTOR/AGONIST / alpha helical sandwhich / nuclear receptor / family five / transcription factor / co-activator / TRANSCRIPTION-RECEPTOR-AGONIST complex
Function / homology
Function and homology information


Regulation of gene expression in early pancreatic precursor cells / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / tissue development / bile acid metabolic process / embryo development ending in birth or egg hatching / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / homeostatic process / locomotor rhythm ...Regulation of gene expression in early pancreatic precursor cells / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / tissue development / bile acid metabolic process / embryo development ending in birth or egg hatching / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / homeostatic process / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / positive regulation of viral genome replication / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / cellular response to leukemia inhibitory factor / transcription coregulator binding / response to progesterone / cholesterol homeostasis / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / phospholipid binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / regulation of cell population proliferation / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / nuclear body / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear hormone receptor family 5 / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 hormone receptor family 5 / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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-470 / Nuclear receptor subfamily 5 group A member 2 / Nuclear receptor coactivator 2 / FTZ-F1 related protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsWilliams, S.P. / Xu, R. / Zuercher, W.J.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Small Molecule Agonists of the Orphan Nuclear Receptors Steroidogenic Factor-1 (SF-1, NR5A1) and Liver Receptor Homologue-1 (LRH-1, NR5A2).
Authors: Whitby, R.J. / Stec, J. / Blind, R.D. / Dixon, S. / Leesnitzer, L.M. / Orband-Miller, L.A. / Williams, S.P. / Willson, T.M. / Xu, R. / Zuercher, W.J. / Cai, F. / Ingraham, H.A.
History
DepositionNov 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: FTZ-F1 related protein
C: Nuclear receptor coactivator 2
B: FTZ-F1 related protein
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0288
Polymers63,1334
Non-polymers8954
Water5,495305
1
A: FTZ-F1 related protein
C: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0144
Polymers31,5672
Non-polymers4482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-4 kcal/mol
Surface area11380 Å2
MethodPISA
2
B: FTZ-F1 related protein
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0144
Polymers31,5672
Non-polymers4482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-2 kcal/mol
Surface area11930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.667, 89.054, 65.453
Angle α, β, γ (deg.)90.00, 101.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FTZ-F1 related protein


Mass: 29857.574 Da / Num. of mol.: 2 / Fragment: UNP residues 300-541
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR5A2 / Plasmid: pLRH1_LBD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UEC0, UniProt: O00482*PLUS
#2: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1708.931 Da / Num. of mol.: 2 / Fragment: UNP residues 740-753 / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-470 / (3aS,6aR)-5-[(4E)-oct-4-en-4-yl]-N,4-diphenyl-2,3,6,6a-tetrahydropentalen-3a(1H)-amine


Mass: 385.584 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H35N
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M ammonium sulfate, 0.1M sodium acetate trihydrate, 25% w/v polyethylene glycol 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 5, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 3.6 % / Av σ(I) over netI: 37.06 / Number: 195517 / Rmerge(I) obs: 0.035 / Χ2: 1.04 / D res high: 1.75 Å / D res low: 50 Å / Num. obs: 54382 / % possible obs: 91.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.775098.310.0241.263.7
2.993.7710010.0261.1423.8
2.612.9910010.0341.0643.8
2.382.6110010.0451.0063.8
2.22.3810010.0591.0193.8
2.072.210010.0870.9853.8
1.972.0799.610.1330.9643.7
1.891.9793.910.1850.9633.4
1.811.8971.610.2280.9012.7
1.751.8148.210.2680.8342.4
ReflectionResolution: 1.75→50 Å / Num. all: 59760 / Num. obs: 54382 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 18.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.75-1.812.40.26848.2
1.81-1.892.70.22871.6
1.89-1.973.40.18593.9
1.97-2.073.70.13399.6
2.07-2.23.80.087100
2.2-2.383.80.059100
2.38-2.613.80.045100
2.61-2.993.80.034100
2.99-3.773.80.026100
3.77-503.70.02498.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.94 Å
Translation2.5 Å19.94 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→19.94 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 5.294 / SU ML: 0.076 / SU R Cruickshank DPI: 0.1231 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.214 3906 7.2 %RANDOM
Rwork0.185 ---
obs0.187 54326 100 %-
all-59760 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20.91 Å2
2--0.32 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3923 0 66 305 4294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224119
X-RAY DIFFRACTIONr_bond_other_d0.0010.022682
X-RAY DIFFRACTIONr_angle_refined_deg1.0981.9915581
X-RAY DIFFRACTIONr_angle_other_deg0.81636581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2395503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.59624.839186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.81815722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0311518
X-RAY DIFFRACTIONr_chiral_restr0.0560.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024559
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02797
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4841.52489
X-RAY DIFFRACTIONr_mcbond_other0.0991.5997
X-RAY DIFFRACTIONr_mcangle_it0.9423992
X-RAY DIFFRACTIONr_scbond_it1.53331630
X-RAY DIFFRACTIONr_scangle_it2.5654.51582
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 138 -
Rwork0.253 1825 -
obs--100 %
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)
11.2763-0.1455-0.93511.51770.57262.36540.1116-0.16220.18140.0524-0.0141-0.1413-0.09550.1459-0.09750.0744-0.00120.05430.047-0.00940.0927-9.859-5.672-15.524
22.3339-0.5551-1.01551.37030.00121.3662-0.13930.1405-0.3115-0.0381-0.03090.13690.1071-0.04110.17030.08520.00360.0740.0235-0.01370.0963-25.584-1.591-44.379
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A300 - 600
2X-RAY DIFFRACTION1C600 - 900
3X-RAY DIFFRACTION1A1
4X-RAY DIFFRACTION2B300 - 600
5X-RAY DIFFRACTION2D600 - 900
6X-RAY DIFFRACTION2B1

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