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- PDB-4rwv: Crystal structure of PIP3 bound human nuclear receptor LRH-1 (Liv... -

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Basic information

Entry
Database: PDB / ID: 4rwv
TitleCrystal structure of PIP3 bound human nuclear receptor LRH-1 (Liver Receptor Homolog 1, NR5A2) in complex with a co-regulator DAX-1 (NR0B1) peptide at 1.86 A resolution
Components(Nuclear receptor ...) x 2
KeywordsTRANSCRIPTION / Ligand-binding domain of nuclear hormone receptor / PF00104 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for Stem Cell Biology / STEMCELL
Function / homology
Function and homology information


DNA hairpin binding / negative regulation of steroid biosynthetic process / Sertoli 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 / AF-2 domain binding ...DNA hairpin binding / negative regulation of steroid biosynthetic process / Sertoli 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 / AF-2 domain binding / pancreas morphogenesis / gonad development / inner cell mass cell differentiation / pituitary gland development / tissue development / acinar cell differentiation / Sertoli cell development / positive regulation of T cell anergy / positive regulation of stem cell differentiation / negative regulation of intracellular steroid hormone receptor signaling pathway / Leydig cell differentiation / male sex determination / embryonic cleavage / bile acid metabolic process / exocrine pancreas development / negative regulation of chondrocyte differentiation / embryo development ending in birth or egg hatching / cartilage development / adrenal gland development / hypothalamus development / homeostatic process / endodermal cell differentiation / calcineurin-mediated signaling / response to immobilization stress / somatic stem cell population maintenance / positive regulation of viral genome replication / positive regulation of T cell proliferation / neurogenesis / hormone-mediated signaling pathway / cellular response to leukemia inhibitory factor / cholesterol homeostasis / transcription coregulator binding / nuclear receptor binding / negative regulation of DNA-binding transcription factor activity / SUMOylation of intracellular receptors / phospholipid binding / Nuclear Receptor transcription pathway / centriolar satellite / positive regulation of T cell activation / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / male gonad development / transcription corepressor activity / sequence-specific double-stranded DNA binding / intracellular protein localization / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / nuclear speck / ribosome / chromatin remodeling / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / 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 / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / membrane / cytoplasm
Similarity search - Function
Nuclear receptor repeat / Nuclear receptor repeat / 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 receptor repeat / Nuclear receptor repeat / 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-PIZ / Nuclear receptor subfamily 0 group B member 1 / Nuclear receptor subfamily 5 group A member 2 / Nuclear receptor subfamily 0 group B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.859 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology / Partnership for Stem Cell Biology (STEMCELL)
CitationJournal: To be published
Title: Crystal structure of a Homo sapiens hepatocytic transcription factor hB1F-2 (B1F2) in complex with nuclear receptor subfamily 0 group B member 1 (NR0B1, residues 140-154) from human at 1.86 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology
History
DepositionDec 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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 DAX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8689
Polymers30,3852
Non-polymers1,4837
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint2 kcal/mol
Surface area13650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.616, 50.187, 93.608
Angle α, β, γ (deg.)90.000, 109.220, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-813-

HOH

21A-889-

HOH

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Components

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Nuclear receptor ... , 2 types, 2 molecules AB

#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: 28733.102 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN (UNP residues 294-551)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B1F, CPF, FTF, NR5A2, RC2754B.LRH_1 / Plasmid: pRSF-2 Ek/LIC ligation independent cloning / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O00482
#2: Protein/peptide Nuclear receptor DAX1 / Nuclear receptor subfamily 0 / group B / member 1


Mass: 1651.904 Da / Num. of mol.: 1 / Fragment: UNP residues 140-154 / Source method: obtained synthetically / Details: comes from screening buffer as a peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: F1D8P4, UniProt: P51843*PLUS

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Non-polymers , 4 types, 233 molecules

#3: Chemical ChemComp-PIZ / (2S)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane -1,2-diyl dihexadecanoate / PI(3,4,5)P3 dipalmitoyl (16:0, 16:0)


Mass: 1050.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H82O22P4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsLRH-1 (UNIPROT O00482, LIVER RECEPTOR HOMOLOG 1, NUCLEAR RECEPTOR SUBFAMILY 5 GROUP A MEMBER 2, ...LRH-1 (UNIPROT O00482, LIVER RECEPTOR HOMOLOG 1, NUCLEAR RECEPTOR SUBFAMILY 5 GROUP A MEMBER 2, NR5A2_HUMAN) LIGAND BINDING DOMAIN (LBD) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MAHHHHHHVDDDDKMSENLYFQS. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A SERINE (S) FOLLOWED BY AMINO ACID RESIDUES 294-541 OF THE TARGET SEQUENCE. PEPTIDE CORRESPONDING TO THE DAX1 (NUCLEAR RECEPTOR DAX1, NR0B1, UNIPROT F1D8P4_HUMAN) RESIDUES 140-PRQGSILYSLLTSSK-154 WAS CO-CRYSTALLIZED WITH THE LRH-1 LBD

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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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: LRH-1/PIP3, 20% PEG 4K, 0.2M NaOAc, 0.1M Tris (8.5), 0.036mM PIP3, 0.90mM 15-mer PRQGSILYSLLTSSK, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→29.463 Å / Num. obs: 25922 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.31 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 11.72
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.85-1.920.5771.913331433178
1.92-1.990.4032.915929470897.1
1.99-2.080.274.216195502995.5
2.08-2.190.1726.418450518298
2.19-2.330.128.817962520297.7
2.33-2.510.08910.916759509196.6
2.51-2.760.06714.118078511797.9
2.76-3.160.05417.817912520698.3
3.16-3.980.0522.817678509396.3
3.980.05125.217499506896.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
PHASER2.3.0phasing
XSCALEJuly 4, 2012 BUILT=20130617data scaling
PHENIX1.8.2refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YOK

1yok


Resolution: 1.859→29.463 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.23 / σ(F): 1.14 / Phase error: 22.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 1296 5 %
Rwork0.1707 --
obs0.1726 25914 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.47 Å2 / Biso mean: 39.0131 Å2 / Biso min: 13.9 Å2
Refinement stepCycle: LAST / Resolution: 1.859→29.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2087 0 95 226 2408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122320
X-RAY DIFFRACTIONf_angle_d1.3323145
X-RAY DIFFRACTIONf_chiral_restr0.085354
X-RAY DIFFRACTIONf_plane_restr0.005389
X-RAY DIFFRACTIONf_dihedral_angle_d23.489968
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8595-1.93390.31791400.26282621276194
1.9339-2.02190.2591410.20992726286798
2.0219-2.12850.20091410.19362714285597
2.1285-2.26180.21381490.17522756290598
2.2618-2.43630.20741460.16772744289098
2.4363-2.68140.25251390.18122720285998
2.6814-3.0690.2371410.17092792293399
3.069-3.86530.18971500.15692727287797
3.8653-29.46680.18911490.16132818296797
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)
11.9460.3575-0.08411.82990.31462.9916-0.0517-0.11080.0033-0.01880.01520.07560.01440.03990.03160.1438-0.0152-0.00030.14650.00760.1889-0.936639.193127.2948
24.65251.3655-1.40143.91482.15092.2825-0.3032-0.0952-0.83360.4371-0.03480.12830.7878-0.22480.29510.3635-0.09730.07370.2067-0.0140.3781-15.632327.386535.0438
36.69550.93944.16384.97311.6917.9150.2828-0.3265-0.06510.45890.28980.12060.43860.3133-0.52930.31020.07470.06530.39990.01420.25529.14943.189843.6405
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 297:539A297 - 539
2X-RAY DIFFRACTION2chain B and resid 140:154B140 - 154
3X-RAY DIFFRACTION3chain A and resid 601:6010

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