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- PDB-4qjr: Crystal structure of human nuclear receptor sf-1 (nr5a1) bound to... -

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Basic information

Entry
Database: PDB / ID: 4qjr
TitleCrystal structure of human nuclear receptor sf-1 (nr5a1) bound to its hormone pip3 at 2.4 a resolution
Components
  • Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
  • Steroidogenic factor 1
KeywordsTRANSCRIPTION FACTOR/HORMONE / NUCLEAR HORMONE RECEPTOR / NR5A1 / SF-1 LIGAND BINDINGNUCLEAR DOMAIN / REGULATORY LIGANDS / TRANSCRIPTION / TRANSCRIPTION REGULATION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY / PARTNERSHIP FOR STEM CELL BIOLOGY / PIP3 / PIP2 / NUCLEUS / NUCLEAR PHOSPHATIDYLINOSITOL PHOSPHATES / TRANSCRIPTION FACTOR-HORMONE complex / STEMCELL
Function / homology
Function and homology information


primary sex determination / response to gonadotropin-releasing hormone / Sertoli cell differentiation / negative regulation of female gonad development / luteinization / regulation of steroid biosynthetic process / sex determination / positive regulation of male gonad development / Regulation of MITF-M dependent genes involved in metabolism / Transcriptional regulation of testis differentiation ...primary sex determination / response to gonadotropin-releasing hormone / Sertoli cell differentiation / negative regulation of female gonad development / luteinization / regulation of steroid biosynthetic process / sex determination / positive regulation of male gonad development / Regulation of MITF-M dependent genes involved in metabolism / Transcriptional regulation of testis differentiation / tissue development / Transcriptional regulation of pluripotent stem cells / Leydig cell differentiation / positive regulation of fatty acid oxidation / male sex determination / cellular respiration / maintenance of protein location in nucleus / hormone metabolic process / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / adrenal gland development / response to starvation / temperature homeostasis / female gonad development / lncRNA binding / response to muscle activity / intracellular glucose homeostasis / fatty acid oxidation / calcineurin-mediated signaling / response to dietary excess / adipose tissue development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / brown fat cell differentiation / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / energy homeostasis / digestion / hormone-mediated signaling pathway / positive regulation of gluconeogenesis / SUMOylation of transcription cofactors / RNA splicing / nuclear receptor binding / transcription coregulator binding / gluconeogenesis / respiratory electron transport chain / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / mitochondrion organization / transcription initiation at RNA polymerase II promoter / SUMOylation of intracellular receptors / circadian regulation of gene expression / negative regulation of smooth muscle cell proliferation / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / regulation of circadian rhythm / PML body / phospholipid binding / chromatin DNA binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / mRNA processing / sequence-specific double-stranded DNA binding / Regulation of RUNX2 expression and activity / : / positive regulation of cold-induced thermogenesis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / cellular response to oxidative stress / protein-containing complex assembly / neuron apoptotic process / sequence-specific DNA binding / DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / protein stabilization / RNA polymerase II cis-regulatory region sequence-specific DNA binding / ubiquitin protein ligase binding / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Nuclear hormone receptor family 5 / PGC-1alpha, RNA recognition motif / PGC-1 / Retinoid X Receptor / Retinoid X Receptor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily ...Nuclear hormone receptor family 5 / PGC-1alpha, RNA recognition motif / PGC-1 / Retinoid X Receptor / Retinoid X Receptor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding 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 / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Chem-PIZ / Steroidogenic factor 1 / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology (STEMCELL)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: The signaling phospholipid PIP3 creates a new interaction surface on the nuclear receptor SF-1.
Authors: Blind, R.D. / Sablin, E.P. / Kuchenbecker, K.M. / Chiu, H.J. / Deacon, A.M. / Das, D. / Fletterick, R.J. / Ingraham, H.A.
History
DepositionJun 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.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_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_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 1.5Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Steroidogenic factor 1
B: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5965
Polymers29,4272
Non-polymers1,1693
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-12 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.850, 74.850, 139.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-502-

ACT

21A-502-

ACT

31A-690-

HOH

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Components

#1: Protein Steroidogenic factor 1 / SF-1 / STF-1 / Adrenal 4-binding protein / Fushi tarazu factor homolog 1 / Nuclear receptor ...SF-1 / STF-1 / Adrenal 4-binding protein / Fushi tarazu factor homolog 1 / Nuclear receptor subfamily 5 group A member 1 / Steroid hormone receptor Ad4BP


Mass: 27903.406 Da / Num. of mol.: 1 / Fragment: UNP residues 218-461 / Mutation: C247S, C412S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AD4BP, FTZF1, NR5A1, RC2003B, SF1 / Plasmid: pBH4 / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13285
#2: Protein/peptide Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / PGC-1-alpha / PPAR-gamma coactivator 1-alpha / PPARGC-1-alpha / Ligand effect modulator 6


Mass: 1523.854 Da / Num. of mol.: 1 / Fragment: UNP residues 139-152 / Source method: obtained synthetically
Details: PGC-1ALPHA (PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA CO-ACTIVATOR-1ALPHA) PEPTIDE CONTAINING RESIDUES 139-EEPSLLKKLLLAPA-152
Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2
#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
Details: SMILES string: CCCCCCCCCCCCCCCC(=O)OCC(CO[P](O)(=O)OC1C(O)C (O[P](O)(O)=O)C(O[P](O)(O)=O)C(O[P](O)(O)=O)C1O)OC(=O)CCCCCCCCCCCCCCC
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSF-1 (UNIPROT Q13285, NR5A1_HUMAN, STF1_HUMAN) LIGAND BINDING DOMAIN (LBD) WAS EXPRESSED WITH AN N- ...SF-1 (UNIPROT Q13285, NR5A1_HUMAN, STF1_HUMAN) LIGAND BINDING DOMAIN (LBD) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY AMINO ACID RESIDUES 218-461 OF THE TARGET SEQUENCE. RESIDUES C247 AND C412 IN THIS SF-1 CONSTRUCT WERE MUTATED TO S247 AND S412. PEPTIDE CORRESPONDING TO THE PGC-1ALPHA (PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA CO-ACTIVATOR-1ALPHA) RESIDUES 139-EEPSLLKKLLLAPA-152 WAS CO-CRYSTALLIZED WITH THE SF-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: 3.32 Å3/Da / Density % sol: 62.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10% PEG 8K, 0.025M MGOAC, 30% GLYCEROL, 0.067MM PIP3, 0.80MM 14MER EEPSLLKKLLLAPA, NANODROP, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K

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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 2, 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: 2.4→29.165 Å / Num. all: 16205 / Num. obs: 16205 / % possible obs: 99.6 % / Redundancy: 11.9 % / Rsym value: 0.043 / Net I/σ(I): 24.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.468.90.711.11012011360.7198.5
2.46-2.5311.80.6061.31347011460.60699.6
2.53-2.612.10.4131.91345011100.41399.7
2.6-2.68120.3562.21292710750.35699.8
2.68-2.7712.60.25331334010570.25399.7
2.77-2.8712.30.1873.91248910180.18799.9
2.87-2.98110.1365.2107799840.136100
2.98-3.112.70.1155.9120479450.115100
3.1-3.2412.90.0926.9118739220.092100
3.24-3.3912.90.0757.7113698820.075100
3.39-3.5812.60.0658.7106798450.065100
3.58-3.7911.60.05410.691187890.05499.8
3.79-4.0611.90.0511.787127340.0598.7
4.06-4.3813.30.04512.694797150.045100
4.38-4.812.70.0414.582406510.04100
4.8-5.3711.70.03815.470836050.038100
5.37-6.211.10.03816.159665370.03899.9
6.2-7.5912.10.03715.956434670.03799.9
7.59-10.7310.70.02718.139763700.02799.6
10.73-29.16510.40.0261522642170.02694.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
PHENIX1.8.2_1309refinement
SCALA3.3.20data scaling
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YOW

1yow


Resolution: 2.4→29.165 Å / Occupancy max: 1 / Occupancy min: 0.17 / SU ML: 0.24 / σ(F): 2.03 / Phase error: 26.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2296 803 4.99 %
Rwork0.1895 --
obs0.1914 16099 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.66 Å2 / Biso mean: 76.3499 Å2 / Biso min: 34.79 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 75 117 2230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022222
X-RAY DIFFRACTIONf_angle_d0.5893021
X-RAY DIFFRACTIONf_chiral_restr0.04351
X-RAY DIFFRACTIONf_plane_restr0.002380
X-RAY DIFFRACTIONf_dihedral_angle_d20.036925
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4001-2.55030.26371300.23852461259199
2.5503-2.7470.26781290.21172495262499
2.747-3.0230.24341330.214225182651100
3.023-3.45940.30651340.215525342668100
3.4594-4.35460.23081350.19142564269999
4.3546-24.74670.20181420.17327242866100
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)
12.5078-0.93350.21231.9678-0.61142.07880.09890.1923-0.22870.0035-0.0720.12220.34810.042200.5098-0.139-0.03960.333-0.06950.4013-19.772727.9725-3.3137
20.1430.095-0.04080.0529-0.04230.02250.1380.2865-0.3304-0.12630.06590.28410.19890.02690.19580.6688-0.6059-0.36330.6082-0.07591.5518-35.946818.6027-8.7738
30.06090.00370.06050.03510.02880.0385-0.38370.23090.51910.09320.05590.6417-1.2718-0.185400.8711-0.0814-0.03470.50940.04510.6006-23.52544.9193-11.872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resseq 218:461)A218 - 461
2X-RAY DIFFRACTION2chain B and (resseq 141:152)B141 - 152
3X-RAY DIFFRACTION3chain A and (resseq 501:501)A501

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