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- PDB-3f5c: Structure of Dax-1:LRH-1 complex -

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Basic information

Entry
Database: PDB / ID: 3f5c
TitleStructure of Dax-1:LRH-1 complex
Components
  • Nuclear receptor subfamily 0 group B member 1
  • Nuclear receptor subfamily 5 group A member 2
KeywordsTRANSCRIPTION / nuclear receptor / transcriptional corepressor / regulatory complex / DNA-binding / Lipid-binding / Metal-binding / Nucleus / Receptor / Transcription regulation / Zinc / Zinc-finger / Cytoplasm / Repressor
Function / homology
Function and homology information


DNA hairpin binding / pancreas morphogenesis / Sertoli cell differentiation / negative regulation of intracellular steroid hormone receptor signaling pathway / negative regulation of steroid biosynthetic process / zygotic genome activation / positive regulation of tendon cell differentiation / SUMOylation of intracellular receptors / inner cell mass cell differentiation / primary ovarian follicle growth ...DNA hairpin binding / pancreas morphogenesis / Sertoli cell differentiation / negative regulation of intracellular steroid hormone receptor signaling pathway / negative regulation of steroid biosynthetic process / zygotic genome activation / positive regulation of tendon cell differentiation / SUMOylation of intracellular receptors / inner cell mass cell differentiation / primary ovarian follicle growth / morula formation / positive regulation of glucocorticoid biosynthetic process / Nuclear Receptor transcription pathway / AF-2 domain binding / positive regulation of T cell anergy / sex determination / Leydig cell differentiation / gonad development / male sex determination / tissue development / Sertoli cell development / positive regulation of stem cell differentiation / exocrine pancreas development / bile acid metabolic process / embryonic cleavage / cellular response to leukemia inhibitory factor / negative regulation of chondrocyte differentiation / cartilage development / adrenal gland development / somatic stem cell population maintenance / transcription factor binding / response to immobilization stress / calcineurin-mediated signaling / negative regulation of gluconeogenesis / centriolar satellite / positive regulation of viral genome replication / neurogenesis / hormone-mediated signaling pathway / cholesterol homeostasis / positive regulation of T cell proliferation / epithelial cell differentiation / nuclear receptor binding / transcription coregulator binding / male gonad development / negative regulation of inflammatory response / phospholipid binding / RNA polymerase II transcription regulator complex / nuclear receptor activity / positive regulation of T cell activation / intracellular protein localization / sequence-specific double-stranded DNA binding / transcription corepressor activity / regulation of cell population proliferation / chromosome / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / cell differentiation / nuclear speck / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / ribosome / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA-templated transcription / DNA binding / RNA binding / nucleoplasm / zinc ion binding / membrane / nucleus / cytosol / 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
Nuclear receptor subfamily 5 group A member 2 / Nuclear receptor subfamily 0 group B member 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFletterick, R.J. / Sablin, E.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: The structure of corepressor Dax-1 bound to its target nuclear receptor LRH-1.
Authors: Sablin, E.P. / Woods, A. / Krylova, I.N. / Hwang, P. / Ingraham, H.A. / Fletterick, R.J.
History
DepositionNov 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear receptor subfamily 5 group A member 2
B: Nuclear receptor subfamily 0 group B member 1
C: Nuclear receptor subfamily 0 group B member 1


Theoretical massNumber of molelcules
Total (without water)89,4823
Polymers89,4823
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.355, 103.355, 117.455
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Nuclear receptor subfamily 5 group A member 2 / Liver receptor homolog 1 / LRH-1


Mass: 28731.969 Da / Num. of mol.: 1 / Fragment: UNP residues 313-560 / Mutation: I525L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nr5a2, Lrh1 / Plasmid: pACYCDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: P45448
#2: Protein Nuclear receptor subfamily 0 group B member 1 / Nuclear receptor DAX-1


Mass: 30375.004 Da / Num. of mol.: 2 / Fragment: UNP residues 205-472
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nr0b1, Ahch, Dax1 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: Q61066

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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: 3.51 Å3/Da / Density % sol: 64.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 20% PEG 8000, 1 mM Deoxy-BigChap, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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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 315 / Detector: CCD / Date: Nov 4, 2005 / Details: mirrors
RadiationMonochromator: KHOZU Double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. all: 24752 / Num. obs: 24366 / % possible obs: 98.44 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.8
Reflection shellResolution: 3→3.1 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
CNSrefinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PK5

1pk5


Resolution: 3→24.785 Å / SU ML: 0.59 / σ(F): 0.08 / Phase error: 33.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2792 700 2.87 %
Rwork0.222 --
obs0.2236 24366 98.44 %
all-24752 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.487 Å2 / ksol: 0.273 e/Å3
Refinement stepCycle: LAST / Resolution: 3→24.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4936 0 0 0 4936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115036
X-RAY DIFFRACTIONf_angle_d1.2536813
X-RAY DIFFRACTIONf_dihedral_angle_d15.3821863
X-RAY DIFFRACTIONf_chiral_restr0.073781
X-RAY DIFFRACTIONf_plane_restr0.006861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.23140.40251150.38274579X-RAY DIFFRACTION95
3.2314-3.55580.33931390.34749X-RAY DIFFRACTION99
3.5558-4.06830.27861430.22024730X-RAY DIFFRACTION99
4.0683-5.11820.23421740.16674745X-RAY DIFFRACTION99
5.1182-24.78610.25671290.18734863X-RAY DIFFRACTION100
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)
15.4661-1.69361.48935.5721-0.01463.6729-0.2929-0.47080.88020.90520.1252-0.5328-0.38660.14420.08450.4680.1362-0.23370.3151-0.26720.437884.906941.126169.0478
25.69630.6719-0.59443.48321.13992.94960.19130.1125-0.0504-0.1627-0.12640.08860.14190.1101-0.02610.36060.1241-0.17580.31210.21930.142956.003143.500247.575
30.39340.7796-0.97655.1574.40036.1197-0.2029-0.1129-0.1102-0.08060.129-0.462-0.01850.2999-0.02210.19470.0271-0.06270.3417-0.24440.651487.90323.93245.0439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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