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- PDB-5syz: Human Liver Receptor Homologue-1 (LRH-1) Bound to a RJW100 stereo... -

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Basic information

Entry
Database: PDB / ID: 5syz
TitleHuman Liver Receptor Homologue-1 (LRH-1) Bound to a RJW100 stereoisomer and a Fragment of TIF-2
Components
  • Nuclear receptor coactivator 2
  • Nuclear receptor subfamily 5 group A member 2
KeywordsNUCLEAR PROTEIN / Nuclear receptor / agonist / coactivator
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 / regulation of cellular response to insulin stimulus / 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 / cellular response to leukemia inhibitory factor / 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 / response to progesterone / cholesterol homeostasis / transcription coregulator binding / nuclear receptor binding / phospholipid 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 / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / 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 / transcription cis-regulatory region binding / nuclear body / protein dimerization activity / 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 / chromatin / regulation of DNA-templated transcription / 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 / 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. / Nuclear receptor coactivator, interlocking / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Retinoid X Receptor / Retinoid X Receptor / 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-71W / 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: 1.9261 Å
AuthorsOrtlund, E.A. / Mays, S.G.
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 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
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
DepositionAug 12, 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 6, 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: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1703
Polymers29,7832
Non-polymers3871
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-7 kcal/mol
Surface area12170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.312, 46.312, 219.966
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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: 27973.240 Da / Num. of mol.: 1
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 Nuclear receptor coactivator 2 / / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1810.035 Da / Num. of mol.: 1 / Fragment: UNP Rresidues 740-754 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-71W / (1S,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.: 51 / 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: 1.98 Å3/Da / Density % sol: 37.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Sodium acetate, PEG4000, glycerol

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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: Jul 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.926→50 Å / Num. obs: 19170 / % possible obs: 99.7 % / Redundancy: 11.1 % / Biso Wilson estimate: 35.61 Å2 / Rmerge(I) obs: 0.074 / Net I/av σ(I): 33.533 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.93-28.20.6870.861197.9
2-2.088.90.4750.93199.8
2.08-2.179.80.330.9691100
2.17-2.2910.60.2330.9871100
2.29-2.4311.30.1820.9941100
2.43-2.6211.90.1430.9941100
2.62-2.8812.40.1050.9971100
2.88-3.312.70.0780.9981100
3.3-4.16130.0580.999199.9
4.16-5012.10.0560.998199.4

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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: 5L11

5l11


Resolution: 1.9261→35.423 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.05
RfactorNum. reflection% reflection
Rfree0.2277 1336 7 %
Rwork0.2047 --
obs0.2063 19073 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 134 Å2 / Biso mean: 50.5847 Å2 / Biso min: 22.67 Å2
Refinement stepCycle: final / Resolution: 1.9261→35.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 63 51 2130
Biso mean--59.17 43.27 -
Num. residues----248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042087
X-RAY DIFFRACTIONf_angle_d0.5882819
X-RAY DIFFRACTIONf_chiral_restr0.035320
X-RAY DIFFRACTIONf_plane_restr0.003357
X-RAY DIFFRACTIONf_dihedral_angle_d13.3161267
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9261-1.99490.29281230.28011638176196
1.9949-2.07480.29251300.247317241854100
2.0748-2.16920.24931310.231417351866100
2.1692-2.28350.25761300.218117391869100
2.2835-2.42650.24571340.214117711905100
2.4265-2.61380.23561340.214317651899100
2.6138-2.87680.24231330.213317811914100
2.8768-3.29280.24791340.208117861920100
3.2928-4.14760.20781390.179218351974100
4.1476-35.42950.20591480.199619632111100
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)
17.32354.35763.25552.87192.69815.59710.4321-0.2555-0.23550.9884-0.16920.47040.5644-0.1339-0.24340.37050.0389-0.05690.2568-0.03310.40680.0076-26.383417.6881
27.34054.78460.98674.02662.3313.38940.1512-0.60820.7310.3757-0.201-0.1646-0.49980.3173-0.03150.56060.04570.00710.3907-0.04980.540613.81480.822527.8001
33.47940.13871.49082.37780.042.32880.22950.2324-0.12750.1275-0.2081-0.06760.09580.33380.02380.25840.08340.00530.25540.0160.193113.2984-15.000816.0265
42.25090.1716-1.21523.7527-1.39062.9519-0.2282-0.06520.4737-0.37510.17590.4648-0.5009-0.1925-0.09890.56550.0792-0.12410.2883-0.03580.49333.21533.542314.4291
56.01944.99580.89954.15180.83290.85-0.21620.27440.5219-0.51140.07030.4671-0.2912-0.1245-0.02340.47480.1619-0.06570.44280.0860.42273.8964-3.25863.8828
63.65390.1505-0.34253.71390.25962.35650.1220.7792-0.224-0.2011-0.1730.2860.1993-0.02740.09880.42830.1879-0.07760.3756-0.09160.28353.8796-24.56736.5811
73.46311.77940.04541.88920.21290.43650.09510.68480.172-0.3479-0.1229-0.0898-0.18230.3492-0.00690.48220.16020.01590.59250.12630.354116.5948-8.28476.9504
86.74872.00180.02243.3519-2.43543.59350.7956-0.2994-0.51560.2821-0.6227-0.33081.07110.787-0.40370.3584-0.0143-0.12720.3925-0.05280.363924.1008-19.723523.504
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 300 through 314 )A300 - 314
2X-RAY DIFFRACTION2chain 'A' and (resid 315 through 340 )A315 - 340
3X-RAY DIFFRACTION3chain 'A' and (resid 341 through 397 )A341 - 397
4X-RAY DIFFRACTION4chain 'A' and (resid 398 through 421 )A398 - 421
5X-RAY DIFFRACTION5chain 'A' and (resid 422 through 440 )A422 - 440
6X-RAY DIFFRACTION6chain 'A' and (resid 441 through 494 )A441 - 494
7X-RAY DIFFRACTION7chain 'A' and (resid 495 through 538 )A495 - 538
8X-RAY DIFFRACTION8chain 'C' and (resid 742 through 752 )C742 - 752

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