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- PDB-4qk4: Crystal structure of human nuclear receptor sf-1 (nr5a1) bound to... -

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Basic information

Entry
Database: PDB / ID: 4qk4
TitleCrystal structure of human nuclear receptor sf-1 (nr5a1) bound to pip2 at 2.8 a resolution
Components
  • Peroxisome proliferator-activated receptor gamma coactivator 1-alphaPeroxisome proliferator-activated receptor gamma
  • Steroidogenic factor 1
KeywordsTRANSCRIPTION FACTOR/HORMONE / NUCLEAR HORMONE RECEPTOR / NR5A1 / SF-1 LIGAND BINDING 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 / positive regulation of mitochondrial DNA metabolic process / positive regulation of muscle tissue development / sex determination / regulation of steroid biosynthetic process / positive regulation of male gonad development / Transcriptional regulation of testis differentiation ...primary sex determination / response to gonadotropin-releasing hormone / Sertoli cell differentiation / negative regulation of female gonad development / positive regulation of mitochondrial DNA metabolic process / positive regulation of muscle tissue development / sex determination / regulation of steroid biosynthetic process / positive regulation of male gonad development / Transcriptional regulation of testis differentiation / luteinization / calcineurin-mediated signaling / positive regulation of cellular respiration / Transcriptional regulation of pluripotent stem cells / positive regulation of fatty acid oxidation / tissue development / Leydig cell differentiation / : / male sex determination / maintenance of protein location in nucleus / : / hormone metabolic process / lncRNA binding / cellular respiration / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / temperature homeostasis / adrenal gland development / female gonad development / response to starvation / positive regulation of ATP biosynthetic process / response to dietary excess / intracellular glucose homeostasis / fatty acid oxidation / adipose tissue development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / energy homeostasis / brown fat cell differentiation / positive regulation of gluconeogenesis / digestion / respiratory electron transport chain / hormone-mediated signaling pathway / mitochondrion organization / RNA splicing / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / negative regulation of smooth muscle cell proliferation / gluconeogenesis / transcription coregulator binding / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / phospholipid binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / SUMOylation of intracellular receptors / Heme signaling / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PML body / PPARA activates gene expression / chromatin DNA binding / mRNA processing / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / male gonad development / Regulation of RUNX2 expression and activity / nuclear receptor activity / positive regulation of DNA-binding transcription factor activity / Circadian Clock / sequence-specific double-stranded DNA binding / cellular response to oxidative stress / positive regulation of cold-induced thermogenesis / protein-containing complex assembly / neuron apoptotic process / DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / transcription coactivator activity / protein stabilization / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / ubiquitin protein ligase binding / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / 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
PGC-1alpha, RNA recognition motif / PGC-1 / Nuclear hormone receptor family 5 / 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 ...PGC-1alpha, RNA recognition motif / PGC-1 / Nuclear hormone receptor family 5 / 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 / 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 / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-PIK / Steroidogenic factor 1 / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.81 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 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Mar 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

Downloads & links

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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)30,7098
Polymers29,4272
Non-polymers1,2816
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-9 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.000, 75.000, 138.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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 / Peroxisome proliferator-activated receptor gamma / 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-PIK / (2S)-3-{[(R)-hydroxy{[(1R,2R,3S,4R,5R,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dihexadecanoate / PI(4,5)P2 dipalmitoyl (16:0,16:0)


Mass: 970.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H81O19P3
Details: SMILES string: CCCCCCCCCCCCCCCC(=O)OCC(CO[P](O)(=O)OC1C(O)C(O)C (O[P](O)(O)=O)C(O[P](O)(O)=O)C1O)OC(=O)CCCCCCCCCCCCCCC
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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 (UNIPROT Q9UBK2, PRGC1_HUMAN)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: 3.31 Å3/Da / Density % sol: 62.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: SF-1, 6% PEG 8000, 0.2M MGOAC, 20% ETHYLENE GLYCOL, 0.067MM PIP2, 0.80MM 14-MER EEPSLLKKLLLAPA, NANODROP, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002+ / Wavelength: 1.5418
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Sep 16, 2013 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.81→29.119 Å / Num. obs: 10167 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 90.29 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 23.72
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.81-2.910.6562.89279182599.8
2.91-3.030.4563.99715190699.7
3.03-3.160.2816.38816172699.7
3.16-3.330.16510.29608187799.7
3.33-3.540.10315.49422184299.5
3.54-3.810.06523.39258183099.4
3.81-4.190.04532.29123181399.6
4.19-4.790.03440.49363183599.6
4.79-60.02945.79504182499.5
60.01956.49829186997.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
PHASER2.3.0phasing
XSCALEdata scaling
PHENIX1.8.2refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YOW

1yow


Resolution: 2.81→29.119 Å / Occupancy max: 1 / Occupancy min: 0.32 / SU ML: 0.43 / σ(F): 2 / Phase error: 28.14 / Stereochemistry target values: ML
Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. 1,2-ETHANEDIOL (EDO) FROM THE CRYSTALLIZATION SOLUTION HAS BEEN ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. 1,2-ETHANEDIOL (EDO) FROM THE CRYSTALLIZATION SOLUTION HAS BEEN MODELED IN THE SOLVENT STRUCTURE. 3. PIP2 WAS CO-CRYSTALLIZED WITH THE SF-1 PROTEIN AND PGC-1ALPHA PEPTIDE.
RfactorNum. reflection% reflection
Rfree0.2408 506 4.99 %
Rwork0.1997 --
obs0.2017 10138 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.41 Å2 / Biso mean: 73.8761 Å2 / Biso min: 31.06 Å2
Refinement stepCycle: LAST / Resolution: 2.81→29.119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2041 0 83 55 2179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022183
X-RAY DIFFRACTIONf_angle_d0.542947
X-RAY DIFFRACTIONf_chiral_restr0.036344
X-RAY DIFFRACTIONf_plane_restr0.003366
X-RAY DIFFRACTIONf_dihedral_angle_d19.46895
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8101-3.09240.39311230.271523452468100
3.0924-3.53870.31571250.235323662491100
3.5387-4.45420.24311260.197423972523100
4.4542-24.76710.19691320.17932524265699
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)
12.8304-1.3020.24513.137-1.25092.20740.06520.2173-0.31010.0231-0.02610.22610.3523-0.0104-0.02830.5194-0.1629-0.0340.416-0.08570.4029-19.869928.1049-3.6273
25.2053.16261.6643.6018-2.07486.9410.03790.5511-0.5179-0.41420.27670.04840.34730.0987-0.28081.092-0.5508-0.23870.9516-0.17871.4315-36.088618.8358-8.7622
35.76342.7543-2.87316.89551.2345.9489-0.12920.96280.9020.21730.25090.997-0.8343-1.1967-0.11390.368-0.0094-0.01110.7210.10630.3239-23.743644.259-11.6308
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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