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- PDB-4ple: Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound t... -

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Basic information

Entry
Database: PDB / ID: 4ple
TitleHuman Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to an E. Coli Phospholipid and a Fragment of TIF-2
Components
  • Nuclear receptor coactivator 2
  • Nuclear receptor subfamily 5 group A member 2
KeywordsTRANSCRIPTION / Nuclear Receptor / phospholipid
Function / homology
Function and homology information


positive regulation of glucocorticoid biosynthetic process / zygotic genome activation / positive regulation of tendon cell differentiation / morula formation / Regulation of gene expression in early pancreatic precursor cells / primary ovarian follicle growth / pancreas morphogenesis / inner cell mass cell differentiation / tissue development / acinar cell differentiation ...positive regulation of glucocorticoid biosynthetic process / zygotic genome activation / positive regulation of tendon cell differentiation / morula formation / Regulation of gene expression in early pancreatic precursor cells / primary ovarian follicle growth / pancreas morphogenesis / inner cell mass cell differentiation / tissue development / acinar cell differentiation / Sertoli cell development / positive regulation of stem cell differentiation / positive regulation of T cell anergy / embryonic cleavage / bile acid metabolic process / embryo development ending in birth or egg hatching / exocrine pancreas development / cartilage development / negative regulation of chondrocyte differentiation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / homeostatic process / locomotor rhythm / calcineurin-mediated signaling / aryl hydrocarbon receptor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / somatic stem cell population maintenance / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / positive regulation of viral genome replication / cellular response to hormone stimulus / Recycling of bile acids and salts / transcription regulator inhibitor activity / hormone-mediated signaling pathway / : / positive regulation of adipose tissue development / neurogenesis / Regulation of lipid metabolism by PPARalpha / positive regulation of T cell proliferation / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / cholesterol homeostasis / cellular response to leukemia inhibitory factor / nuclear receptor binding / transcription coregulator binding / negative regulation of smoothened signaling pathway / SUMOylation of intracellular receptors / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Cytoprotection by HMOX1 / phospholipid binding / positive regulation of T cell activation / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / : / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / transcription regulator complex / Estrogen-dependent gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / transcription cis-regulatory region binding / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / DNA-binding transcription factor activity / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / 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 / 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-EPH / Nuclear receptor subfamily 5 group A member 2 / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.752 Å
AuthorsOrtlund, E.A. / Musille, P.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)RO1DK095750 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)T32ES012870 United States
American Heart Association12PRE12060583 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Unexpected Allosteric Network Contributes to LRH-1 Co-regulator Selectivity.
Authors: Musille, P.M. / Kossmann, B.R. / Kohn, J.A. / Ivanov, I. / Ortlund, E.A.
History
DepositionMay 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Nuclear receptor subfamily 5 group A member 2
B: Nuclear receptor coactivator 2
C: Nuclear receptor subfamily 5 group A member 2
D: Nuclear receptor coactivator 2
E: Nuclear receptor subfamily 5 group A member 2
F: Nuclear receptor coactivator 2
G: Nuclear receptor subfamily 5 group A member 2
H: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,14124
Polymers119,9228
Non-polymers10,21816
Water6,864381
1
A: Nuclear receptor subfamily 5 group A member 2
B: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5356
Polymers29,9812
Non-polymers2,5554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-15 kcal/mol
Surface area12810 Å2
MethodPISA
2
C: Nuclear receptor subfamily 5 group A member 2
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9205
Polymers29,9812
Non-polymers1,9403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-16 kcal/mol
Surface area12850 Å2
MethodPISA
3
E: Nuclear receptor subfamily 5 group A member 2
F: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7658
Polymers29,9812
Non-polymers3,7846
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-19 kcal/mol
Surface area12920 Å2
MethodPISA
4
G: Nuclear receptor subfamily 5 group A member 2
H: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9205
Polymers29,9812
Non-polymers1,9403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-15 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.947, 76.885, 108.482
Angle α, β, γ (deg.)90.000, 95.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nuclear receptor subfamily 5 group A member 2 / Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F / CYP7A promoter-binding factor ...Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F / CYP7A promoter-binding factor / Hepatocytic transcription factor / Liver receptor homolog 1 / LRH-1


Mass: 28271.668 Da / Num. of mol.: 4 / Fragment: UNP residues 301-541
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR5A2, B1F, CPF, FTF / Production host: Escherichia coli (E. coli) / References: UniProt: O00482
#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.: 4 / Fragment: UNP residues 740-753 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical
ChemComp-EPH / L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE


Mass: 709.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H68NO8P / Comment: phospholipid*YM
#4: Chemical
ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.7-1 M di-Sodium Malonate, 0.1 M HEPES pH 7.4, 0.5% Jeffamine ED-2001
PH range: 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9999 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 19, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.752→46.62 Å / Num. obs: 100330 / % possible obs: 92.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 21.78 Å2 / Rmerge(I) obs: 0.066 / Χ2: 1.384 / Net I/av σ(I): 21.517 / Net I/σ(I): 12.77 / Num. measured all: 365113
Reflection shellResolution: 1.752→1.814 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 3.2 / Num. unique all: 6751 / Χ2: 0.982 / Rejects: 0 / % possible all: 62.76

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YOK

1yok


Resolution: 1.752→46.62 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 1993 1.99 %Random selection
Rwork0.2141 98056 --
obs0.2145 100049 92.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.55 Å2 / Biso mean: 31.6418 Å2 / Biso min: 11.55 Å2
Refinement stepCycle: final / Resolution: 1.752→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8130 0 493 381 9004
Biso mean--35.2 35.6 -
Num. residues----1001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048816
X-RAY DIFFRACTIONf_angle_d0.70711951
X-RAY DIFFRACTIONf_chiral_restr0.0261400
X-RAY DIFFRACTIONf_plane_restr0.0041461
X-RAY DIFFRACTIONf_dihedral_angle_d14.1773563
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7517-1.79550.2769930.27094585467861
1.7955-1.84410.27861080.25355282539070
1.8441-1.89830.27631210.25345943606479
1.8983-1.95960.27781360.2546715685189
1.9596-2.02960.25581490.23057284743397
2.0296-2.11090.25121530.225875567709100
2.1109-2.2070.21911550.219175767731100
2.207-2.32330.24581530.213675357688100
2.3233-2.46890.23491540.214875957749100
2.4689-2.65950.23921530.223975737726100
2.6595-2.92710.25521540.22275657719100
2.9271-3.35060.26771550.221876067761100
3.3506-4.22090.19451560.188876437799100
4.2209-46.63640.2241530.19857598775198
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)
12.58080.1450.78260.51620.25282.56030.0765-0.1026-0.0153-0.0004-0.02020.06090.0469-0.308-0.04910.1092-0.002-0.00080.15510.01110.1459-40.6604-14.897216.9768
23.18962.6597-0.32163.13012.04445.8939-0.0650.0485-0.47080.2849-0.17130.14960.4169-0.0040.18560.50710.0549-0.1250.1765-0.07680.354-46.6616-32.811413.8875
32.31780.13690.44640.60930.03282.71430.010.0944-0.0090.02390.0129-0.03380.01210.1261-0.01110.08540.00180.01120.12030.00860.1283-63.46523.279537.1834
45.9991-4.692-0.86053.67860.41567.8825-0.174-0.0265-0.7799-0.0466-0.14780.23111.0195-0.24260.35640.5259-0.0682-0.12330.17590.07920.3667-58.35265.320841.4627
52.5331-0.03240.81760.44070.19572.6153-0.02380.1380.0096-0.06560.05340.0353-0.01390.1171-0.01980.1074-0.0030.01130.13150.00020.123-50.8332-11.932556.5927
61.1248-0.357-0.34795.7003-3.40554.5149-0.05160.08260.29460.28180.0075-0.0105-0.46280.0624-0.14830.3791-0.1027-0.1650.23860.24130.4404-51.93976.598351.2613
71.8024-0.0540.31550.39910.4043.08480.01940.0761-0.0383-0.03750.0780.0038-0.03350.2113-0.07920.1032-0.01030.01760.13870.00010.1225-78.5708-12.16792.4411
85.0780.1811.00987.0298-3.0878.1919-0.17510.06830.53110.1555-0.03510.0102-0.57510.00050.01690.4998-0.0822-0.10320.20310.12440.2783-79.85636.109-3.6462
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 298:538)A298 - 538
2X-RAY DIFFRACTION2(chain B and resseq 742:750)B742 - 750
3X-RAY DIFFRACTION3(chain C and resseq 299:538)C299 - 538
4X-RAY DIFFRACTION4(chain D and resseq 742:751)D742 - 751
5X-RAY DIFFRACTION5(chain E and resseq 297:537)E297 - 537
6X-RAY DIFFRACTION6(chain F and resseq 742:751)F742 - 751
7X-RAY DIFFRACTION7(chain G and resseq 298:538)G298 - 538
8X-RAY DIFFRACTION8(chain H and resseq 742:751)H742 - 751

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