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- PDB-5l11: Human Liver Receptor Homologue-1 (LRH-1) Bound to RJW100 and a Fr... -

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Basic information

Entry
Database: PDB / ID: 5l11
TitleHuman Liver Receptor Homologue-1 (LRH-1) Bound to RJW100 and a Fragment of TIF-2
Components
  • Nuclear receptor subfamily 5 group A member 2
  • Tif2
Keywordstranscription/inhibitor / nuclear receptor / agonist / transcription-inhibitor complex
Function / homology
Function and homology information


Regulation of gene expression in early pancreatic precursor cells / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / tissue development / bile acid metabolic process / embryo development ending in birth or egg hatching / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / homeostatic process / locomotor rhythm ...Regulation of gene expression in early pancreatic precursor cells / pancreas morphogenesis / calcineurin-mediated signaling / acinar cell differentiation / tissue development / bile acid metabolic process / embryo development ending in birth or egg hatching / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / homeostatic process / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / positive regulation of viral genome replication / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Recycling of bile acids and salts / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / regulation of cellular response to insulin stimulus / hormone-mediated signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / cellular response to leukemia inhibitory factor / transcription coregulator binding / response to progesterone / cholesterol homeostasis / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / phospholipid binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / regulation of cell population proliferation / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / nuclear body / protein dimerization activity / 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 / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear hormone receptor family 5 / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 ...Nuclear hormone receptor family 5 / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-RJW / Nuclear receptor subfamily 5 group A member 2 / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 Å
AuthorsMays, S.G. / Ortlund, E.A.
Funding support United States, 3items
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 General Medical Sciences (NIH/NIGMS)T32GM008602 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)F31DK111171 United States
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Crystal Structures of the Nuclear Receptor, Liver Receptor Homolog 1, Bound to Synthetic Agonists.
Authors: Mays, S.G. / Okafor, C.D. / Whitby, R.J. / Goswami, D. / Stec, J. / Flynn, A.R. / Dugan, M.C. / Jui, N.T. / Griffin, P.R. / Ortlund, E.A.
History
DepositionJul 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Dec 14, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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: Tif2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4263
Polymers30,0402
Non-polymers3871
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-6 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.418, 46.418, 220.259
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-789-

HOH

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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: Enterobacteria phage L1 (virus) / References: UniProt: O00482
#2: Protein/peptide Tif2


Mass: 1708.931 Da / Num. of mol.: 1 / Fragment: unp residues 740-753 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596*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


Mass: 18.015 Da / Num. of mol.: 92 / 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: 1.97 Å3/Da / Density % sol: 37.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.05 M Sodium Acetate, pH 4.6, PEG 4000 5-11%, glycerol 5-10%

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.849→50 Å / Num. obs: 21130 / % possible obs: 96.8 % / Redundancy: 8.9 % / Biso Wilson estimate: 30.49 Å2 / Rmerge(I) obs: 0.094 / Net I/av σ(I): 28.466 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.85-1.926.80.5820.878186.1
1.92-1.997.70.4460.94192.6
1.99-2.088.30.3420.97196.1
2.08-2.198.20.2480.981197.1
2.19-2.338.20.1890.989197.6
2.33-2.518.10.1520.994198.5
2.51-2.768.60.1260.992199.9
2.76-3.1610.20.1120.9951100
3.16-3.9911.30.0920.997199.9
3.99-5010.50.0690.997199.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PLZ

3plz


Resolution: 1.849→35.491 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.19
RfactorNum. reflection% reflection
Rfree0.2413 1470 6.99 %
Rwork0.198 --
obs0.2011 21026 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 146.84 Å2 / Biso mean: 42.147 Å2 / Biso min: 19.69 Å2
Refinement stepCycle: final / Resolution: 1.849→35.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 63 92 2149
Biso mean--34.84 36.57 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042075
X-RAY DIFFRACTIONf_angle_d0.5782803
X-RAY DIFFRACTIONf_chiral_restr0.035318
X-RAY DIFFRACTIONf_plane_restr0.002355
X-RAY DIFFRACTIONf_dihedral_angle_d11.7821261
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8488-1.90850.32911140.28921504161885
1.9085-1.97670.25291240.25691649177392
1.9767-2.05580.30541290.23671714184396
2.0558-2.14940.25481310.22921743187497
2.1494-2.26270.25051320.21311748188097
2.2627-2.40440.24551320.21091769190198
2.4044-2.590.27231390.21091827196699
2.59-2.85060.25241370.21218241961100
2.8506-3.26280.22821390.201118581997100
3.2628-4.10980.20271410.168118882029100
4.1098-35.4970.24491520.18432032218499
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)
12.73342.739-1.14658.1549-2.31032.74490.189-0.0744-0.3450.7044-0.1776-0.19590.1113-0.1499-0.00790.33310.0399-0.02270.2872-0.00380.259814.62632.81223.979
22.6311-0.0559-0.86793.4250.03832.23120.17530.2040.13150.1443-0.18860.0108-0.0749-0.2090.03150.18720.0612-0.00460.2021-0.00070.13859.81238.16816.026
31.63820.86731.81335.5283.39623.52-0.0289-0.019-0.1849-0.21050.1203-0.46110.43440.2561-0.0170.43310.09340.07610.26370.0310.378219.90219.64514.435
42.5722.1405-1.87842.1916-1.64361.3961-0.29620.3475-0.5849-0.36550.2651-0.42450.27530.0981-0.0830.3480.10790.06150.3134-0.06160.354119.19926.2813.831
53.4544-0.0124-0.29463.3425-0.45263.01350.06510.63120.1735-0.0886-0.1166-0.3111-0.06850.00420.05230.33490.14550.06190.28460.05510.23419.25547.8016.535
64.91353.6382-1.30973.7336-0.95750.6890.06870.4271-0.2046-0.2499-0.15220.0465-0.0806-0.3040.05330.41530.1495-0.01120.4708-0.09670.252210.28432.6493.561
75.57734.13772.49683.24252.84417.00220.31130.0952-0.25410.3432-0.38320.53010.1273-0.7430.25890.2896-0.0104-0.02180.3937-0.09990.2894-1.12628.09314.937
85.0645-0.6103-1.84357.31041.45823.63740.69220.0560.3340.008-0.4378-0.0009-0.4543-0.3758-0.18580.29930.00310.10310.27770.01690.2642-0.98942.87123.486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 300:340 )A300 - 340
2X-RAY DIFFRACTION2( CHAIN A AND RESID 341:397 )A341 - 397
3X-RAY DIFFRACTION3( CHAIN A AND RESID 398:421 )A398 - 421
4X-RAY DIFFRACTION4( CHAIN A AND RESID 422:440 )A422 - 440
5X-RAY DIFFRACTION5( CHAIN A AND RESID 441:494 )A441 - 494
6X-RAY DIFFRACTION6( CHAIN A AND RESID 495:522 )A495 - 522
7X-RAY DIFFRACTION7( CHAIN A AND RESID 523:536 )A523 - 536
8X-RAY DIFFRACTION8( CHAIN C AND RESID 742:752 )C742 - 752

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