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- PDB-7jyd: Human Liver Receptor Homolog-1 in Complex with 10CA and a Fragmen... -

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Basic information

Entry
Database: PDB / ID: 7jyd
TitleHuman Liver Receptor Homolog-1 in Complex with 10CA and a Fragment of Tif2
Components
  • Nuclear receptor coactivator 2
  • Nuclear receptor subfamily 5 group A member 2
KeywordsTRANSCRIPTION / agonist / nuclear receptor
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 / 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
Similarity search - Domain/homology
Chem-VQA / 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: 2.3 Å
AuthorsD'Agostino, E.H. / Mays, S.G. / Ortlund, E.A.
Funding support United States, 7items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE-1444932 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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008367-27 United States
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)R01DK114213 United States
United States Department of Agriculture (USDA)3092-5-001-057 United States
CitationJournal: To Be Published
Title: Tapping into a phospholipid-LRH-1 axis yields a powerful anti-inflammatory agent with in vivo activity against colitis
Authors: D'Agostino, E.H. / Mays, S.G. / Flynn, A.F. / Huang, X. / Wang, G. / Liu, X. / Millings, E.J. / Okafor, C.D. / Patel, A. / Cato, M.L. / Cornelison, J.C. / Houtman, R. / Moore, D.D. / ...Authors: D'Agostino, E.H. / Mays, S.G. / Flynn, A.F. / Huang, X. / Wang, G. / Liu, X. / Millings, E.J. / Okafor, C.D. / Patel, A. / Cato, M.L. / Cornelison, J.C. / Houtman, R. / Moore, D.D. / Calvert, J.W. / Jui, N.T. / Ortlund, E.A.
History
DepositionAug 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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)30,3533
Polymers29,8812
Non-polymers4731
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Fluorescence polarization binding assay
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-7 kcal/mol
Surface area12220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.370, 88.370, 105.674
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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: 28401.771 Da / Num. of mol.: 1 / Fragment: nuclear receptor ligand-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR5A2, B1F, CPF, FTF / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: 1478.756 Da / Num. of mol.: 1 / Fragment: residues 740-751 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-VQA / 10-[(3aR,6R,6aR)-6-hydroxy-3-phenyl-3a-(1-phenylethenyl)-1,3a,4,5,6,6a-hexahydropentalen-2-yl]decanoic acid


Mass: 472.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H40O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.99 Å3/Da / Density % sol: 69.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.4 M sodium/potassium tartrate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 21672 / % possible obs: 100 % / Redundancy: 15.8 % / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.045 / Rrim(I) all: 0.177 / Χ2: 1.233 / Net I/σ(I): 5.9 / Num. measured all: 343073
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.3815.31.16421330.7760.3051.2040.486100
2.38-2.4814.20.88321250.860.240.9160.541100
2.48-2.5916.30.69521540.9290.1760.7170.593100
2.59-2.7317.30.49521190.9640.1220.510.715100
2.73-2.9170.36921420.980.0920.3810.885100
2.9-3.1216.50.28321630.9850.0710.2921.07100
3.12-3.4415.50.20121540.990.0530.2081.458100
3.44-3.9315.30.13821700.990.0360.1431.803100
3.93-4.9516.70.12821970.9940.0330.1322.222100
4.95-5014.30.15123150.9910.0410.1572.53499.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12-2829-000refinement
PDB_EXTRACT3.25data extraction
PHENIXdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L11

5l11


Resolution: 2.3→40.77 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 1087 5.02 %
Rwork0.189 20553 -
obs0.191 21640 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.51 Å2 / Biso mean: 74.1224 Å2 / Biso min: 35.06 Å2
Refinement stepCycle: final / Resolution: 2.3→40.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2033 0 74 34 2141
Biso mean--67.03 65.82 -
Num. residues----250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032115
X-RAY DIFFRACTIONf_angle_d0.5182858
X-RAY DIFFRACTIONf_dihedral_angle_d7.296284
X-RAY DIFFRACTIONf_chiral_restr0.035322
X-RAY DIFFRACTIONf_plane_restr0.003362
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.410.27171350.24712494262999
2.41-2.530.26331320.214725412673100
2.53-2.690.25071350.22125482683100
2.69-2.90.22741360.194125322668100
2.9-3.190.23611330.223525502683100
3.19-3.650.20251370.193525952732100
3.65-4.60.21041350.170925942729100
4.6-40.770.23731440.175626992843100
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)
18.0267-0.38171.19024.32355.9448.4649-0.17150.48510.8683-0.9682-0.23910.9025-0.9279-0.07320.52080.6548-0.0962-0.07050.55120.16990.715221.6347-18.1056-23.9521
25.77944.83832.79636.19882.72974.6707-0.0358-0.67211.45980.5547-0.30111.0327-0.8499-0.52440.4550.7890.04080.0090.5218-0.13190.752727.9045-2.5171-2.443
34.9955.1531-2.1138.6717-0.70777.6889-0.1687-0.07020.1221-0.1004-0.06680.52370.004-0.40980.20460.501-0.0594-0.06810.4155-0.0170.438927.2659-19.3587-9.0635
49.7186-2.08996.08177.5002-3.51634.5781-0.58821.21220.8692-0.4018-0.13410.1117-0.98161.09230.61460.8871-0.1922-0.07360.56490.00940.575741.738-0.9124-10.692
57.04994.95274.60839.1935.70325.1344-0.57590.9143-0.36050.00530.627-0.6420.11641.5279-0.45030.4297-0.1670.01910.5008-0.06050.42245.7786-12.3416-12.7566
67.07833.5453-0.95997.0827-1.43059.00070.05120.5305-0.3708-0.177-0.0297-0.2778-0.01020.3650.08510.3352-0.093-0.03170.4058-0.05280.354230.1664-25.6291-19.8108
74.47722.75263.37947.06465.26014.29090.1942-0.2878-0.27990.99510.6214-0.44811.45010.7341-0.6710.4073-0.0477-0.07180.31910.02560.395440.2589-19.7277-6.4258
82.97753.74063.15295.1744.31073.72290.6365-2.35110.66481.8641-0.80120.1414-0.0132-0.7470.57740.9216-0.0874-0.05611.026-0.06880.850531.1924-12.066.8949
93.52772.4807-2.62812.8017-0.8033.00190.212-2.21270.96721.8347-0.21181.25410.4557-1.8325-0.08210.771-0.24950.19051.062-0.21270.888217.3889-17.87732.1252
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 299 through 314 )A299 - 314
2X-RAY DIFFRACTION2chain 'A' and (resid 315 through 362 )A315 - 362
3X-RAY DIFFRACTION3chain 'A' and (resid 363 through 397 )A363 - 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 522 )A495 - 522
8X-RAY DIFFRACTION8chain 'A' and (resid 523 through 538 )A523 - 538
9X-RAY DIFFRACTION9chain 'C' and (resid 742 through 751 )C742 - 751

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