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- PDB-3f7d: SF-1 LBD bound by phosphatidylcholine -

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Basic information

Entry
Database: PDB / ID: 3f7d
TitleSF-1 LBD bound by phosphatidylcholine
Components
  • Peroxisome proliferator-activated receptor gamma coactivator 1-alphaPeroxisome proliferator-activated receptor gamma
  • nuclear receptor SF-1
KeywordsTRANSCRIPTION / nuclear receptor / coactivator peptide / ligand / phospholipid / phosphatidylcholine / transcriptional regulation / DNA-binding / Metal-binding / Nucleus / Receptor / Transcription regulation / Zinc-finger / Activator / RNA-binding
Function / homology
Function and homology information


flavone metabolic process / : / : / positive regulation of cellular metabolic process / response to metformin / response to norepinephrine / : / euchromatin => GO:0000791 / cellular response to resveratrol / cellular response to nitrite ...flavone metabolic process / : / : / positive regulation of cellular metabolic process / response to metformin / response to norepinephrine / : / euchromatin => GO:0000791 / cellular response to resveratrol / cellular response to nitrite / response to gonadotropin-releasing hormone / positive regulation of progesterone biosynthetic process / Sertoli cell differentiation / response to electrical stimulus involved in regulation of muscle adaptation / reproductive process / : / cellular response to ionomycin / SUMOylation of intracellular receptors / negative regulation of female gonad development / Nuclear Receptor transcription pathway / positive regulation of mitochondrial DNA metabolic process / positive regulation of muscle tissue development / skeletal muscle atrophy / sex determination / response to methionine / positive regulation of male gonad development / positive regulation of podocyte apoptotic process / negative regulation of smooth muscle cell migration / luteinization / adaptive thermogenesis / calcineurin-mediated signaling / : / positive regulation of cellular respiration / response to xenobiotic stimulus => GO:0009410 / response to epinephrine / positive regulation of fatty acid oxidation / tissue development / chromatin => GO:0000785 / cellular response to fructose stimulus / cellular response to follicle-stimulating hormone stimulus / response to L-leucine / cellular response to potassium ion / autophagy of mitochondrion / Leydig cell differentiation / galactose metabolic process / : / male sex determination / apical dendrite / maintenance of protein location in nucleus / cellular response to interleukin-6 / hormone metabolic process / cellular response to thyroid hormone stimulus / negative regulation of glycolytic process / peroxisome proliferator activated receptor binding / response to muscle activity / adrenal gland development / female gonad development / positive regulation of ATP biosynthetic process / response to starvation / cellular response to caffeine / fatty acid oxidation / regulation of NMDA receptor activity / response to dietary excess / transcription factor binding / alpha-tubulin binding / androgen metabolic process / negative regulation of mitochondrial fission / adipose tissue development / energy homeostasis / brown fat cell differentiation / forebrain development / negative regulation of signaling receptor activity / cellular response to transforming growth factor beta stimulus / respiratory electron transport chain / response to cold / hormone-mediated signaling pathway / cerebellum development / mitochondrion organization / cytosolic ribosome / response to reactive oxygen species / nuclear receptor coactivator activity / negative regulation of protein phosphorylation / response to activity / cellular response to estradiol stimulus / response to ischemia / gluconeogenesis / promoter-specific chromatin binding / transcription coregulator binding / nuclear estrogen receptor binding / nuclear receptor binding / cellular response to glucose stimulus / transcription coregulator activity / negative regulation of smooth muscle cell proliferation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of smooth muscle cell proliferation / phospholipid binding / circadian regulation of gene expression / regulation of circadian rhythm / PML body / chromatin DNA binding
Similarity search - Function
Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / 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 ...Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / 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-P42 / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / Steroidogenic factor 1 / Steroidogenic factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSablin, E.P. / Fletterick, R.J.
CitationJournal: Mol.Endocrinol. / Year: 2009
Title: Structure of SF-1 bound by different phospholipids: evidence for regulatory ligands.
Authors: Sablin, E.P. / Blind, R.D. / Krylova, I.N. / Ingraham, J.G. / Cai, F. / Williams, J.D. / Fletterick, R.J. / Ingraham, H.A.
History
DepositionNov 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 2, 2014Group: Source and taxonomy
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 20, 2021Group: 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 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 SF-1
B: Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2583
Polymers29,4922
Non-polymers7661
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-11 kcal/mol
Surface area12630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.895, 67.228, 82.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein nuclear receptor SF-1 / Steroidogenic factor-1 / Nuclear receptor subfamily 5 / group A / member 1


Mass: 27968.135 Da / Num. of mol.: 1 / Fragment: UNP residues 219-462 / Mutation: C302S, C408S, C413S, C423S, C267(CAF)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nr5a1, Ftzf1, RP23-354G20.5-001 / Production host: Escherichia coli (E. coli) / References: UniProt: Q812G5, UniProt: P33242*PLUS
#2: Protein/peptide Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / Peroxisome proliferator-activated receptor gamma / PPAR-gamma coactivator 1-alpha / PPARGC-1-alpha / PGC-1-alpha


Mass: 1523.854 Da / Num. of mol.: 1 / Fragment: UNP residues 137-150 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: O70343
#3: Chemical ChemComp-P42 / (2S)-2-{[(1R)-1-hydroxyhexadecyl]oxy}-3-{[(1R)-1-hydroxyoctadecyl]oxy}propyl 2-(trimethylammonio)ethyl phosphate / 1-Stearoyl-2-Palmitoyl-sn-Glycero-3-Phosphocholine


Mass: 766.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H88NO8P / Comment: SPPC, phospholipid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.21 Å3/Da / Density % sol: 44.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate, 20% PEG 3350, 0.2 M sodium acetate, 2 mM TCEP, 10% xylitol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Jun 25, 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: 2.2→25 Å / Num. all: 13803 / Num. obs: 13232 / % possible obs: 95.86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 15.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.24 / % possible all: 89.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
CNSrefinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDb entry 1YMT

1ymt


Resolution: 2.2→23.76 Å / SU ML: 0.32 / σ(F): 0.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 399 3.02 %
Rwork0.18 --
obs0.182 13232 95.9 %
all-13803 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.77 Å2 / ksol: 0.34 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→23.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 52 123 2171
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.006
X-RAY DIFFRACTIONf_dihedral_angle_d
X-RAY DIFFRACTIONf_chiral_restr
X-RAY DIFFRACTIONf_plane_restr
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.51820.26641300.21583989X-RAY DIFFRACTION92
2.5182-3.17150.26171200.19384303X-RAY DIFFRACTION97
3.1715-23.76380.22181490.16064541X-RAY DIFFRACTION99
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)
10.92790.0403-0.05321.59210.32221.0437-0.0001-0.0051-0.0471-0.13370.04420.1078-0.0475-0.0151-0.03880.03260.0037-0.00680.03250.02390.0348-76.298940.7911-25.0635
20.02810.03280.0790.38120.10110.30920.02070.0954-0.0768-0.2550.01210.1732-0.03430.09520.02970.4318-0.0579-0.12520.323-0.21360.2899-84.573635.9774-42.0542
3-0.25940.17990.04310.17590.03270.06520.15650.1275-0.07350.03060.2819-0.1042-0.0386-0.1714-0.36170.15020.02980.0320.32120.050.2854-61.552236.7247-28.7616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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