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- PDB-5unj: Structure of Human Liver Receptor Homolog 1 in complex with PGC1a... -

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Basic information

Entry
Database: PDB / ID: 5unj
TitleStructure of Human Liver Receptor Homolog 1 in complex with PGC1a and RJW100
Components
  • Nuclear receptor subfamily 5 group A member 2
  • Peroxisome proliferator-activated gamma coactivator 1-alpha
KeywordsNUCLEAR PROTEIN / Nuclear receptor / agonist / coregulator
Function / homology
Function and homology information


Regulation of gene expression in early pancreatic precursor cells / positive regulation of mitochondrial DNA metabolic process / positive regulation of muscle tissue development / pancreas morphogenesis / calcineurin-mediated signaling / positive regulation of cellular respiration / acinar cell differentiation / positive regulation of fatty acid oxidation / tissue development / : ...Regulation of gene expression in early pancreatic precursor cells / positive regulation of mitochondrial DNA metabolic process / positive regulation of muscle tissue development / pancreas morphogenesis / calcineurin-mediated signaling / positive regulation of cellular respiration / acinar cell differentiation / positive regulation of fatty acid oxidation / tissue development / : / bile acid metabolic process / : / lncRNA binding / cellular respiration / response to muscle activity / embryo development ending in birth or egg hatching / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / temperature homeostasis / homeostatic process / positive regulation of ATP biosynthetic process / response to starvation / intracellular glucose homeostasis / fatty acid oxidation / response to dietary excess / adipose tissue development / positive regulation of viral genome replication / 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 / cellular response to leukemia inhibitory factor / hormone-mediated signaling pathway / mitochondrion organization / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / RNA splicing / cholesterol homeostasis / gluconeogenesis / transcription coregulator binding / transcription initiation at RNA polymerase II promoter / nuclear receptor binding / transcription coregulator activity / negative regulation of smooth muscle cell proliferation / 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 / 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 / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / protein-containing complex assembly / neuron apoptotic process / DNA-binding transcription factor binding / Estrogen-dependent gene expression / negative regulation of neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription coactivator activity / protein stabilization / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / 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 / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
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-RJW / Nuclear receptor subfamily 5 group A member 2 / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.959 Å
AuthorsMays, S.G. / Ortlund, E.A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK095750 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)F31DK111171 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008602 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH K12GM000680 United States
CitationJournal: Mol. Pharmacol. / Year: 2017
Title: Structure and Dynamics of the Liver Receptor Homolog 1-PGC1 alpha Complex.
Authors: Mays, S.G. / Okafor, C.D. / Tuntland, M.L. / Whitby, R.J. / Dharmarajan, V. / Stec, J. / Griffin, P.R. / Ortlund, E.A.
History
DepositionJan 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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: Nuclear receptor subfamily 5 group A member 2
C: Peroxisome proliferator-activated gamma coactivator 1-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2413
Polymers29,8552
Non-polymers3871
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-10 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.180, 84.027, 45.355
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Nuclear receptor subfamily 5 group A member 2 / Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F / CYP7A promoter-binding factor ...Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F / CYP7A promoter-binding factor / Hepatocytic transcription factor / Liver receptor homolog 1 / LRH-1


Mass: 28330.693 Da / Num. of mol.: 1 / Fragment: unp residues 299-541
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR5A2, B1F, CPF, FTF / Production host: Escherichia coli (E. coli) / References: UniProt: O00482
#2: Protein/peptide Peroxisome proliferator-activated gamma coactivator 1-alpha


Mass: 1523.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBK2*PLUS
#3: Chemical ChemComp-RJW / (1R,3aR,6aR)-5-hexyl-4-phenyl-3a-(1-phenylethenyl)-1,2,3,3a,6,6a-hexahydropentalen-1-ol


Mass: 386.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H34O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.05M Sodium acetate, pH 4.6; PEG4000 14%, glycerol 15-21%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jun 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 18170 / % possible obs: 96.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 32.19 Å2 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.042 / Rrim(I) all: 0.108 / Χ2: 0.819 / Net I/σ(I): 7 / Num. measured all: 111677
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-2.0250.3840.9150.1760.4250.48883.8
2.02-2.15.30.3330.6920.1520.3680.52991.6
2.1-2.25.50.2450.9320.1110.270.62196.1
2.2-2.315.80.1990.9840.0880.2180.70298.1
2.31-2.466.10.180.9830.0780.1970.80198.6
2.46-2.656.30.1610.9840.070.1760.94399.4
2.65-2.916.60.1430.9880.060.1550.96599.9
2.91-3.336.80.1260.9940.0520.1371.074100
3.33-4.26.90.0940.9950.0380.1021.043100
4.2-506.70.0710.9960.030.0770.71599.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
PHENIX1.10.1_2155phasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L11

5l11


Resolution: 1.959→42.014 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.84
RfactorNum. reflection% reflection
Rfree0.2265 1270 7.01 %
Rwork0.1993 --
obs0.2012 18122 96.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.1 Å2 / Biso mean: 46.7829 Å2 / Biso min: 22.98 Å2
Refinement stepCycle: final / Resolution: 1.959→42.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 63 58 2031
Biso mean--35.22 42.68 -
Num. residues----236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031974
X-RAY DIFFRACTIONf_angle_d0.4892666
X-RAY DIFFRACTIONf_chiral_restr0.034307
X-RAY DIFFRACTIONf_plane_restr0.003333
X-RAY DIFFRACTIONf_dihedral_angle_d13.7831190
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.959-2.03750.28731150.24921525164080
2.0375-2.13020.21151320.2311753188592
2.1302-2.24250.22271410.20521860200197
2.2425-2.3830.22891420.20541891203398
2.383-2.5670.2151430.20171892203599
2.567-2.82520.25151450.196919342079100
2.8252-3.23390.23141470.211119552102100
3.2339-4.07390.24121470.188319632110100
4.0739-42.02310.20781580.191620792237100
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)
11.86710.424-1.64922.7871-2.03324.84270.00360.10040.26910.04850.22220.2847-0.0071-0.6831-0.23330.2181-0.0216-0.02040.4073-0.04430.3003-17.554722.4518-20.826
22.11760.42040.90352.2878-1.02239.10410.0443-0.3860.00950.0469-0.21740.11970.2494-0.8371-0.0810.27160.0063-0.02070.39540.00810.2923-14.832112.8906-14.9247
36.63382.8659-1.45528.4928-4.49888.28260.01140.5197-0.044-1.44310.350.3376-0.2061-0.89910.02870.43670.009-0.09370.43920.05660.3063-12.390513.4427-35.1051
42.29741.86490.61543.28670.57853.63820.1085-0.2395-0.2683-0.3866-0.0258-0.1001-0.1099-0.15210.03960.22470.0297-0.00290.37530.07910.2642-7.119115.7091-20.4682
53.6845-0.43282.05883.9231-0.80835.5518-0.1218-0.3640.36250.6598-0.31210.1952-0.5975-0.2688-0.00150.3617-0.03990.01480.4395-0.07210.3273-9.892824.885-2.9031
62.40252.0494-0.75782.84240.792.3397-0.0893-0.3198-0.18730.5396-0.174-0.5457-0.25490.07490.26220.2566-0.0191-0.03970.4807-0.02730.33240.939523.9937-8.5749
72.49211.83860.00356.98891.91814.5323-0.02510.0005-0.3095-0.4868-0.0679-0.36450.1238-0.13590.0190.19630.02430.04620.24110.03650.2571-3.602521.023-27.6423
82.78672.06160.82018.43421.19143.937-0.25970.30380.0128-0.5670.2621-0.6932-0.04380.2922-0.05340.25130.03750.07650.31040.00440.31761.072127.3352-33.1167
91.62552.4064-1.67576.8864-4.44444.70230.0979-0.2517-0.326-0.0326-0.4506-0.53840.22970.47590.23350.23240.03890.00510.36550.06640.34531.556814.7462-14.8316
101.0373-0.01261.13033.2306-1.5352.18060.1651-0.7539-0.50450.2979-0.26750.38180.4063-0.4867-0.01090.4349-0.094-0.07080.44810.10150.4465-10.82242.8958-11.0003
115.86230.29082.87446.9582-1.19842.07870.1190.76210.15-1.09940.32860.12760.4306-0.5236-0.05250.4787-0.1569-0.05630.4183-0.03960.3496-17.20393.0498-25.6322
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 300 through 340 )A300 - 340
2X-RAY DIFFRACTION2chain 'A' and (resid 341 through 361 )A341 - 361
3X-RAY DIFFRACTION3chain 'A' and (resid 362 through 370 )A362 - 370
4X-RAY DIFFRACTION4chain 'A' and (resid 371 through 397 )A371 - 397
5X-RAY DIFFRACTION5chain 'A' and (resid 398 through 421 )A398 - 421
6X-RAY DIFFRACTION6chain 'A' and (resid 422 through 440 )A422 - 440
7X-RAY DIFFRACTION7chain 'A' and (resid 441 through 466 )A441 - 466
8X-RAY DIFFRACTION8chain 'A' and (resid 467 through 494 )A467 - 494
9X-RAY DIFFRACTION9chain 'A' and (resid 495 through 522 )A495 - 522
10X-RAY DIFFRACTION10chain 'A' and (resid 523 through 538 )A523 - 538
11X-RAY DIFFRACTION11chain 'C' and (resid 743 through 751 )C743 - 751

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