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- PDB-6vc2: LRH-1 bound to SS-RJW100 and a fragment of the Tif2 Coactivator -

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Basic information

Entry
Database: PDB / ID: 6vc2
TitleLRH-1 bound to SS-RJW100 and a fragment of the Tif2 Coactivator
Components
  • Nuclear receptor coactivator 2
  • Nuclear receptor subfamily 5 group A member 2
KeywordsTRANSCRIPTION / Nuclear hormone receptor
Function / homology
Function and homology information


zygotic genome activation / positive regulation of tendon cell differentiation / inner cell mass cell differentiation / primary ovarian follicle growth / morula formation / Regulation of gene expression in early pancreatic precursor cells / positive regulation of glucocorticoid biosynthetic process / positive regulation of T cell anergy / tissue development / Sertoli cell development ...zygotic genome activation / positive regulation of tendon cell differentiation / inner cell mass cell differentiation / primary ovarian follicle growth / morula formation / Regulation of gene expression in early pancreatic precursor cells / positive regulation of glucocorticoid biosynthetic process / positive regulation of T cell anergy / tissue development / Sertoli cell development / positive regulation of stem cell differentiation / exocrine pancreas development / bile acid metabolic process / embryonic cleavage / embryo development ending in birth or egg hatching / negative regulation of chondrocyte differentiation / homeostatic process / cartilage development / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / somatic stem cell population maintenance / locomotor rhythm / aryl hydrocarbon receptor binding / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / calcineurin-mediated signaling / regulation of lipid metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Recycling of bile acids and salts / transcription regulator inhibitor activity / positive regulation of viral genome replication / neurogenesis / cellular response to hormone stimulus / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / Regulation of lipid metabolism by PPARalpha / response to progesterone / positive regulation of adipose tissue development / positive regulation of T cell proliferation / BMAL1:CLOCK,NPAS2 activates circadian expression / regulation of cellular response to insulin stimulus / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / nuclear receptor binding / transcription coregulator binding / negative regulation of smoothened signaling pathway / SUMOylation of intracellular receptors / circadian regulation of gene expression / Heme signaling / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional activation of mitochondrial biogenesis / negative regulation of inflammatory response / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / phospholipid binding / RNA polymerase II transcription regulator complex / mRNA transcription by RNA polymerase II / nuclear receptor activity / positive regulation of T cell activation / sequence-specific double-stranded DNA binding / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / Estrogen-dependent gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / transcription coactivator activity / protein dimerization activity / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / DNA-binding transcription factor activity / protein domain specific binding / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA-templated transcription / DNA binding / nucleoplasm / zinc ion binding / 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 / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / 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 / Double treble clef zinc finger, C4 type / 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-QU7 / 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: 1.697 Å
AuthorsMays, S.G. / Ortlund, E.A.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01-DK114213 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)NIH F31-DK111171 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01-DK095750 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM008602 United States
National Science Foundation (NSF, United States) United States
CitationJournal: Sci Rep / Year: 2020
Title: Enantiomer-specific activities of an LRH-1 and SF-1 dual agonist.
Authors: Mays, S.G. / Stec, J. / Liu, X. / D'Agostino, E.H. / Whitby, R.J. / Ortlund, E.A.
History
DepositionDec 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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)30,5273
Polymers30,1412
Non-polymers3871
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-7 kcal/mol
Surface area12290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.608, 46.608, 220.890
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: 28330.693 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: Escherichia coli (E. coli) / 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 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-QU7 / (1S,3aS,6aS)-5-hexyl-4-phenyl-3a-(1-phenylethenyl)-1,2,3,3a,6,6a-hexahydropentalen-1-ol / SS-RJW100


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


Mass: 18.015 Da / Num. of mol.: 107 / 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: 1.99 Å3/Da / Density % sol: 38.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Sodium acetate, PEG 4000, glycerol

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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: MAR CCD 130 mm / Detector: CCD / Date: Mar 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.697→50 Å / Num. obs: 27544 / % possible obs: 97.4 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.039 / Rrim(I) all: 0.117 / Χ2: 1.196 / Net I/σ(I): 14.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.763.70.60923140.7880.2920.6820.73284.9
1.76-1.835.70.67626330.8330.2570.730.7994.6
1.83-1.916.70.56726780.9090.2040.6080.95198
1.91-2.026.90.32827390.9570.1160.3511.08198.8
2.02-2.146.80.2127660.980.0740.2241.12799.5
2.14-2.316.70.13827950.9910.0480.1471.40599.7
2.31-2.546.70.09628080.9950.0350.1031.09699.8
2.54-2.916.90.0728310.9960.0260.0751.08999.8
2.91-3.667.70.0828870.9950.0290.0851.26399.8
3.66-508.20.11530930.9910.0410.1221.7998.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L11

5l11


Resolution: 1.697→39.381 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.01
RfactorNum. reflection% reflection
Rfree0.2284 1372 5 %
Rwork0.2096 --
obs0.2105 27434 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.31 Å2 / Biso mean: 38.3136 Å2 / Biso min: 19.48 Å2
Refinement stepCycle: final / Resolution: 1.697→39.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2017 0 58 107 2182
Biso mean--61.52 43.31 -
Num. residues----248
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6975-1.75820.321150.302219385
1.7582-1.82860.30431310.2867249395
1.8286-1.91180.31681340.2669254398
1.9118-2.01260.26931370.2433259799
2.0126-2.13870.24541380.2278262499
2.1387-2.30380.2661390.21632646100
2.3038-2.53560.22891400.21812657100
2.5356-2.90240.21091410.21162679100
2.9024-3.65630.20071440.20712729100
3.6563-39.30.21951530.187290199
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)
10.93-0.5432-0.06080.7611-0.43220.61730.4943-0.52420.21320.8428-0.09650.22930.2641-0.21910.01160.3953-0.0569-0.00350.3257-0.00820.33270.0473-27.008817.5344
21.4752-1.0305-0.34811.2874-0.27531.6527-0.1199-0.11570.63360.37170.1835-0.3904-0.77290.5609-0.00960.4992-0.04450.0360.458-0.08850.435713.78850.726227.8699
33.39820.47961.64020.63551.22822.07950.00790.12740.28620.471-0.02730.1758-0.2650.14550.00170.27710.0110.01010.27860.00460.258114.9551-8.920219.9305
42.10520.2121.07181.8301-0.23191.77180.09720.1355-0.12330.1969-0.0482-0.08070.07930.24150.0010.23960.0417-0.00430.2368-0.02390.221812.5581-18.383313.8894
50.6942-0.0845-0.55310.60510.0380.3475-0.3149-0.01380.26430.04390.08820.6017-0.4695-0.4354-0.00510.35820.0887-0.05490.2967-0.0010.39920.8022-0.449616.833
60.2516-0.04780.28180.5291-0.0570.8108-0.2773-0.16830.19880.21840.0623-0.2201-0.39230.2513-0.0030.520.0704-0.05350.3108-0.0610.38725.85947.397612.4079
70.6741-0.74180.10641.30660.03530.3392-0.17550.30780.5905-0.22680.16740.4168-0.17060.02980.00250.33720.058-0.04380.310.03420.32124.0992-3.03873.8382
81.31170.93831.84042.82730.00593.00760.02090.1934-0.11610.17820.05060.08060.24810.16740.01450.29390.0591-0.05160.2092-0.03270.23077.8994-22.14248.787
90.98621.11160.48942.14370.33073.66740.26270.43870.0473-0.2213-0.19750.28470.1143-0.36950.00140.29650.0963-0.04570.3261-0.09470.30160.1021-27.21484.375
100.9922-0.00010.15031.27030.26160.56450.12540.2368-0.0444-0.1606-0.1733-0.14010.08040.13020.00010.35510.0747-0.00510.39330.07870.249812.9594-9.51023.5298
110.40590.08790.11170.1677-0.0680.36430.00160.22010.0383-0.06250.0487-0.5532-0.12990.204500.3802-0.01770.01980.4190.08650.35924.9309-5.851214.4282
120.91710.15810.61490.77260.33310.41120.4544-0.3079-0.14740.6823-0.3224-0.06180.28880.5447-0.00230.3713-0.0306-0.0780.3708-0.01370.302423.6962-19.708324.4236
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 361 )A341 - 361
4X-RAY DIFFRACTION4chain 'A' and (resid 362 through 397 )A362 - 397
5X-RAY DIFFRACTION5chain 'A' and (resid 398 through 409 )A398 - 409
6X-RAY DIFFRACTION6chain 'A' and (resid 410 through 421 )A410 - 421
7X-RAY DIFFRACTION7chain 'A' and (resid 422 through 440 )A422 - 440
8X-RAY DIFFRACTION8chain 'A' and (resid 441 through 466 )A441 - 466
9X-RAY DIFFRACTION9chain 'A' and (resid 467 through 494 )A467 - 494
10X-RAY DIFFRACTION10chain 'A' and (resid 495 through 522 )A495 - 522
11X-RAY DIFFRACTION11chain 'A' and (resid 523 through 538 )A523 - 538
12X-RAY DIFFRACTION12chain 'C' and (resid 742 through 753 )C742 - 753

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