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- PDB-1pk5: Crystal structure of the orphan nuclear receptor LRH-1 -

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Basic information

Entry
Database: PDB / ID: 1pk5
TitleCrystal structure of the orphan nuclear receptor LRH-1
ComponentsOrphan nuclear receptor NR5A2
KeywordsGENE REGULATION / nuclear receptor / ligand-binding domain / LRH-1
Function / homology
Function and homology information


SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / tissue development / bile acid metabolic process / positive regulation of viral genome replication / hormone-mediated signaling pathway / cholesterol homeostasis ...SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / tissue development / bile acid metabolic process / positive regulation of viral genome replication / hormone-mediated signaling pathway / cholesterol homeostasis / cellular response to leukemia inhibitory factor / transcription coregulator binding / phospholipid binding / RNA polymerase II transcription regulator complex / nuclear receptor activity / regulation of cell population proliferation / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
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 / 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 family 5 / 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
Nuclear receptor subfamily 5 group A member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSablin, E.P. / Krylova, I.N. / Fletterick, R.J. / Ingraham, H.A.
CitationJournal: Mol.Cell / Year: 2003
Title: Structural basis for ligand-independent activation of the orphan nuclear receptor LRH-1
Authors: Sablin, E.P. / Krylova, I.N. / Fletterick, R.J. / Ingraham, H.A.
History
DepositionJun 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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
Remark 999SEQUENCE Author maintains residue I525 in sequence database should be L525

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Orphan nuclear receptor NR5A2
B: Orphan nuclear receptor NR5A2


Theoretical massNumber of molelcules
Total (without water)57,4642
Polymers57,4642
Non-polymers00
Water2,846158
1
A: Orphan nuclear receptor NR5A2


Theoretical massNumber of molelcules
Total (without water)28,7321
Polymers28,7321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Orphan nuclear receptor NR5A2


Theoretical massNumber of molelcules
Total (without water)28,7321
Polymers28,7321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.775, 127.542, 53.213
Angle α, β, γ (deg.)90.00, 91.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Orphan nuclear receptor NR5A2 / Liver receptor homolog / LRH-1


Mass: 28731.969 Da / Num. of mol.: 2 / Fragment: LRH-1 LBD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: NR5A2 OR LRH1 / Plasmid: pBHI-pf1 / Production host: Escherichia coli (E. coli) / References: UniProt: P45448
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: PEG 4000, glycerol, TRIS, isopropanol, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop
215 %glycerol1reservoir
321 %PEG40001reservoir
4100 mMTris1reservoirpH8.8
55 %isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 26, 2002 / Details: KOHZU: DOUBLE CRYSTAL SI(III)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. all: 18102 / Num. obs: 17939 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 45.9 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 24.4
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 5.7 / Rsym value: 0.169 / % possible all: 97.1
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 17954 / % possible obs: 98.2 %
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å / % possible obs: 88.8 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RXR ALPHA (PDB ID 1FBY)

1fby


Resolution: 2.4→24.55 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 693 3.9 %RANDOM
Rwork0.208 ---
all0.215 18102 --
obs0.208 17939 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.3806 Å2 / ksol: 0.355359 e/Å3
Displacement parametersBiso mean: 48.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.18 Å20 Å2-9.52 Å2
2---6.21 Å20 Å2
3---11.39 Å2
Refine analyzeLuzzati coordinate error free: 0.33 Å / Luzzati sigma a free: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.4→24.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3893 0 0 158 4051
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_improper_angle_d1.22
X-RAY DIFFRACTIONc_mcbond_it2.21.5
X-RAY DIFFRACTIONc_mcangle_it3.412
X-RAY DIFFRACTIONc_scbond_it3.562
X-RAY DIFFRACTIONc_scangle_it5.172.5
LS refinement shellResolution: 2.4→2.55 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 114 -
Rwork0.243 2922 -
obs-2922 97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.231 / Rfactor Rwork: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.57
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.22

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