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

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Basic information

Entry
Database: PDB / ID: 1yuc
TitleHuman Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to Phospholipid and a Fragment of Human SHP
Components
  • Nuclear receptor 0B2
  • Orphan nuclear receptor NR5A2
KeywordsTRANSCRIPTION REGULATION / Liver Receptor Homologue 1 / Nuclear Receptor Ligand Binding Domain / LRH-1 / Phospholipid / SHP / Small Heterodimer Partner
Function / homology
Function and homology information


primary ovarian follicle growth / 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 / pancreas morphogenesis / inner cell mass cell differentiation / tissue development / acinar cell differentiation ...primary ovarian follicle growth / 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 / pancreas morphogenesis / inner cell mass cell differentiation / tissue development / acinar cell differentiation / Sertoli cell development / positive regulation of T cell anergy / positive regulation of stem cell differentiation / embryonic cleavage / bile acid metabolic process / exocrine pancreas development / peroxisome proliferator activated receptor binding / negative regulation of chondrocyte differentiation / nuclear thyroid hormone receptor binding / embryo development ending in birth or egg hatching / cartilage development / bile acid and bile salt transport / homeostatic process / calcineurin-mediated signaling / somatic stem cell population maintenance / animal organ regeneration / nuclear retinoid X receptor binding / positive regulation of viral genome replication / transcription regulator inhibitor activity / response to glucose / positive regulation of T cell proliferation / neurogenesis / Notch signaling pathway / hormone-mediated signaling pathway / cholesterol metabolic process / cellular response to leukemia inhibitory factor / cholesterol homeostasis / transcription coregulator binding / negative regulation of DNA-binding transcription factor activity / SUMOylation of intracellular receptors / circadian regulation of gene expression / : / positive regulation of insulin secretion / phospholipid binding / Nuclear Receptor transcription pathway / positive regulation of T cell activation / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / circadian rhythm / transcription corepressor activity / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / Estrogen-dependent gene expression / sequence-specific DNA binding / response to ethanol / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / chromatin remodeling / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein-containing complex binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear receptor subfamily 0 group B member 1/2 / Nuclear hormone receptor family 5 / Retinoid X Receptor / Retinoid X Receptor / 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 receptor subfamily 0 group B member 1/2 / Nuclear hormone receptor family 5 / Retinoid X Receptor / Retinoid X Receptor / 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 subfamily 0 group B member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOrtlund, E.A. / Yoonkwang, L. / Solomon, I.H. / Hager, J.M. / Safi, R. / Choi, Y. / Guan, Z. / Tripathy, A. / Raetz, C.R.H. / McDonnell, D.P. ...Ortlund, E.A. / Yoonkwang, L. / Solomon, I.H. / Hager, J.M. / Safi, R. / Choi, Y. / Guan, Z. / Tripathy, A. / Raetz, C.R.H. / McDonnell, D.P. / Moore, D.D. / Redinbo, M.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Modulation of human nuclear receptor LRH-1 activity by phospholipids and SHP
Authors: Ortlund, E.A. / Lee, Y. / Solomon, I.H. / Hager, J.M. / Safi, R. / Choi, Y. / Guan, Z. / Tripathy, A. / Raetz, C.R.H. / McDonnell, D.P. / Moore, D.D. / Redinbo, M.R.
History
DepositionFeb 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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: Orphan nuclear receptor NR5A2
B: Orphan nuclear receptor NR5A2
C: Nuclear receptor 0B2
D: Nuclear receptor 0B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5159
Polymers61,8194
Non-polymers1,6965
Water4,414245
1
A: Orphan nuclear receptor NR5A2
C: Nuclear receptor 0B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7124
Polymers30,9102
Non-polymers8022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-19 kcal/mol
Surface area12620 Å2
MethodPISA
2
B: Orphan nuclear receptor NR5A2
D: Nuclear receptor 0B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8045
Polymers30,9102
Non-polymers8943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-16 kcal/mol
Surface area12540 Å2
MethodPISA
3
B: Orphan nuclear receptor NR5A2
D: Nuclear receptor 0B2
hetero molecules

A: Orphan nuclear receptor NR5A2
C: Nuclear receptor 0B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5159
Polymers61,8194
Non-polymers1,6965
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
Buried area7380 Å2
ΔGint-45 kcal/mol
Surface area23520 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-37 kcal/mol
Surface area23030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.670, 59.640, 73.240
Angle α, β, γ (deg.)90.00, 100.69, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein Orphan nuclear receptor NR5A2 / Alpha-1-fetoprotein transcription factor / Hepatocytic transcription factor / B1-binding factor / ...Alpha-1-fetoprotein transcription factor / Hepatocytic transcription factor / B1-binding factor / hB1F / CYP7A promoter binding factor / Liver Receptor Homologue 1


Mass: 29459.893 Da / Num. of mol.: 2 / Fragment: Ligand Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR5A2 / Plasmid: PMALCH10T / Production host: Escherichia coli (E. coli) / References: UniProt: O00482
#2: Protein/peptide Nuclear receptor 0B2 / Orphan nuclear receptor SHP / small heterodimer partner


Mass: 1449.673 Da / Num. of mol.: 2 / Fragment: NR Box1 / Source method: obtained synthetically / Details: sequence occurs natuarlly in Homo sapiens / References: UniProt: Q15466
#3: Chemical ChemComp-EPH / L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE


Mass: 709.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H68NO8P / Comment: phospholipid*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.4
Details: 9.5%-15% PEG 3350, 5% glycerol, and 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 100K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2004
RadiationMonochromator: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 42718 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 16.5 Å2 / Rsym value: 0.061 / Net I/σ(I): 22.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 4.15 / Rsym value: 0.309 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data reduction
MOLREPphasing
CNS1.1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→31.28 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 236131.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2082 5 %RANDOM
Rwork0.217 ---
all0.2171 ---
obs0.2171 41458 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.6294 Å2 / ksol: 0.348664 e/Å3
Displacement parametersBiso mean: 26.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.92 Å20 Å23.81 Å2
2---1.14 Å20 Å2
3---5.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→31.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 112 245 4443
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d17.7
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 332 5.1 %
Rwork0.233 6166 -
obs--92.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMPTY.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4GOL.PARION.TOP
X-RAY DIFFRACTION5PTY.PARGOL.PAR

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