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- PDB-7kht: The acyl chains of phosphoinositide PIP3 alter the structure and ... -

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Basic information

Entry
Database: PDB / ID: 7kht
TitleThe acyl chains of phosphoinositide PIP3 alter the structure and function of nuclear receptor Steroidogenic Factor-1 (SF-1)
Components
  • Peroxisome proliferator-activated receptor gamma coactivator 1-alpha peptide
  • Steroidogenic factor 1
KeywordsLIPID BINDING PROTEIN / PI(3 / 4 / 5)P3 acyl chains / acyl chain length / acyl chain induced conformational change / nuclear PIP2 / nuclear PIP3 / nuclear receptor
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 / positive regulation of ATP biosynthetic process / response to starvation / intracellular glucose homeostasis / fatty acid oxidation / response to dietary excess / 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 / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / RNA splicing / gluconeogenesis / transcription coregulator binding / transcription initiation at RNA polymerase II promoter / nuclear receptor binding / transcription coregulator activity / negative regulation of smooth muscle cell proliferation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / phospholipid binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / PML body / 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 / ubiquitin protein ligase binding / chromatin 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 / 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. ...PGC-1alpha, RNA recognition motif / PGC-1 / Nuclear hormone receptor family 5 / 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
Similarity search - Domain/homology
Chem-WES / Steroidogenic factor 1 / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.504 Å
AuthorsBlind, R.D.
Funding support United States, 4items
OrganizationGrant numberCountry
American Cancer SocietyRSG-17-063-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138873 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA243036 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: J.Lipid Res. / Year: 2021
Title: The acyl chains of phosphoinositide PIP3 alter the structure and function of nuclear receptor steroidogenic factor-1.
Authors: Bryant, J.M. / Malabanan, M.M. / Vanderloop, B.H. / Nichols, C.M. / Haratipour, Z. / Poon, K.T. / Sherrod, S.D. / McLean, J.A. / Blind, R.D.
History
DepositionOct 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5303
Polymers29,4272
Non-polymers1,1031
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, PIP3 alters anion exchange mobility due to additional charges on headgroup. Peptide was ordered in structure.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-11 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.349, 65.349, 139.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Steroidogenic factor 1 / / hSF-1 / Adrenal 4-binding protein / Fushi tarazu factor homolog 1 / Nuclear receptor subfamily 5 ...hSF-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 / Mutation: C247S, C412S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR5A1, AD4BP, FTZF1, SF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13285
#2: Protein/peptide Peroxisome proliferator-activated receptor gamma coactivator 1-alpha peptide / PPARGC-1-alpha / Ligand effect modulator 6


Mass: 1523.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2
#3: Chemical ChemComp-WES / (2S)-3-{[(S)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane-1,2-diyl (9E,9'E)di-octadec-9-enoate


Mass: 1103.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H86O22P4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350 and 0.2 M magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.5→38.54 Å / Num. obs: 21999 / % possible obs: 98.38 % / Redundancy: 2 % / Biso Wilson estimate: 70.45 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 21.8
Reflection shellResolution: 2.504→2.594 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1053 / CC1/2: 0.912 / CC star: 0.977 / % possible all: 98.78

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QJR

4qjr


Resolution: 2.504→38.537 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0.23 / Phase error: 32.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 911 4.65 %
Rwork0.2187 --
obs0.2202 19587 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.504→38.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 66 33 2044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012043
X-RAY DIFFRACTIONf_angle_d1.2972767
X-RAY DIFFRACTIONf_dihedral_angle_d20.672816
X-RAY DIFFRACTIONf_chiral_restr0.077335
X-RAY DIFFRACTIONf_plane_restr0.007342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5044-2.63640.39011180.3492683X-RAY DIFFRACTION99
2.6364-2.80150.34221450.34422700X-RAY DIFFRACTION99
2.8015-3.01770.33681530.32592621X-RAY DIFFRACTION99
3.0177-3.32130.2692850.29352720X-RAY DIFFRACTION98
3.3213-3.80150.31981320.23392633X-RAY DIFFRACTION97
3.8015-4.78810.19491250.18432645X-RAY DIFFRACTION98
4.7881-38.5370.21951530.1762674X-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)
17.8918-0.2708-1.06236.28251.47766.35350.18680.00582.55970.89420.32310.8223-1.0608-0.0022-0.53681.3058-0.0170.19740.7380.1141.31335.5001-5.01891.3179
23.7461.46440.27764.39381.79975.42590.5610.94870.6829-1.04670.19790.3659-0.58090.1829-0.45521.20920.0570.01751.1580.32840.977320.389-16.7878-19.0146
35.81880.01351.38.36745.32225.00880.34050.40291.1477-0.71780.6509-1.0328-1.25590.8187-1.04320.9981-0.18250.10280.81880.10660.952323.1721-14.2074-8.3474
42.7717-2.402-1.23296.8342.45754.3302-0.0140.25110.2375-0.20580.0418-0.17980.05020.10620.03140.6534-0.06350.03190.71980.13140.57516.5759-24.6717-7.6782
56.9037-2.5299-1.40633.68810.24274.6004-0.0957-0.29170.01890.13970.1289-0.07990.1337-0.220.03260.6945-0.05760.02010.6363-0.04580.551810.9224-24.0938-0.6914
67.6346-5.0232.11643.3778-0.70586.7625-1.4859-2.85542.0214-0.4760.84-1.8353-0.2377-0.3658-0.00551.1757-0.0341-0.31241.3507-0.27561.403327.4631-12.129812.2857
73.6778-1.9104-2.16145.41822.43695.44120.5183-0.52111.07450.9694-0.25530.2632-0.1840.2673-0.38310.9623-0.06850.05950.7851-0.14780.8227.6388-11.833810.4528
86.9558-3.3564-2.64112.6991.61774.4554-0.5047-1.4835-0.55030.28340.40280.2294-0.140.79180.03920.6372-0.00750.02980.63470.02670.600519.7164-27.93132.2224
92.6163-3.0871-3.02523.90513.81343.7819-0.4349-0.8762-0.1894-0.59460.8907-1.5882-0.33222.7421-0.21770.904-0.04480.10711.2366-0.03521.15233.7464-25.55-8.8927
107.9568-5.21920.4043.46810.07362.44370.11761.47491.1143-0.4723-1.1554-2.45380.15960.38040.57851.4384-0.35310.32761.1834-0.11851.782132.6873-8.906-7.401
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 221 through 232 )
2X-RAY DIFFRACTION2chain 'A' and (resid 233 through 259 )
3X-RAY DIFFRACTION3chain 'A' and (resid 260 through 290 )
4X-RAY DIFFRACTION4chain 'A' and (resid 291 through 341 )
5X-RAY DIFFRACTION5chain 'A' and (resid 342 through 377 )
6X-RAY DIFFRACTION6chain 'A' and (resid 378 through 386 )
7X-RAY DIFFRACTION7chain 'A' and (resid 387 through 414 )
8X-RAY DIFFRACTION8chain 'A' and (resid 415 through 442 )
9X-RAY DIFFRACTION9chain 'A' and (resid 443 through 458 )
10X-RAY DIFFRACTION10chain 'B' and (resid 141 through 152 )

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