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- PDB-4s14: Crystal structure of the orphan nuclear receptor RORgamma ligand-... -

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Basic information

Entry
Database: PDB / ID: 4s14
TitleCrystal structure of the orphan nuclear receptor RORgamma ligand-binding domain in complex with 4alpha-caboxyl, 4beta-methyl-zymosterol (4ACD8)
Components
  • Nuclear receptor ROR-gamma
  • Nuclear receptor-interacting protein 1
KeywordsTRANSCRIPTION / transcription factor
Function / homology
Function and homology information


ovarian follicle rupture / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / lipid storage / nuclear glucocorticoid receptor binding / Peyer's patch development ...ovarian follicle rupture / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / lipid storage / nuclear glucocorticoid receptor binding / Peyer's patch development / positive regulation of circadian rhythm / oxysterol binding / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process / regulation of fat cell differentiation / histone deacetylase complex / regulation of glucose metabolic process / lymph node development / adipose tissue development / nuclear retinoid X receptor binding / xenobiotic metabolic process / SUMOylation of transcription cofactors / cellular response to estradiol stimulus / nuclear estrogen receptor binding / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / fibrillar center / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / Nuclear Receptor transcription pathway / circadian rhythm / transcription corepressor activity / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / Interleukin-4 and Interleukin-13 signaling / Estrogen-dependent gene expression / transcription coactivator activity / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / signaling receptor binding / chromatin / nucleolus / 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 / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Nuclear receptor-interacting protein 1 / Nuclear receptor-interacting protein 1, repression domain 1 / Nuclear receptor-interacting protein 1, repression domain 2 / Nuclear receptor-interacting protein 1, repression domain 3 / Nuclear receptor-interacting protein 1, repression domain 4 / Nuclear receptor-interacting protein 1 repression 1 / Nuclear receptor-interacting protein 1 repression 2 / Nuclear receptor-interacting protein 1 repression 3 / Nuclear receptor-interacting protein 1 repression 4 / Nuclear receptor ROR ...Nuclear receptor-interacting protein 1 / Nuclear receptor-interacting protein 1, repression domain 1 / Nuclear receptor-interacting protein 1, repression domain 2 / Nuclear receptor-interacting protein 1, repression domain 3 / Nuclear receptor-interacting protein 1, repression domain 4 / Nuclear receptor-interacting protein 1 repression 1 / Nuclear receptor-interacting protein 1 repression 2 / Nuclear receptor-interacting protein 1 repression 3 / Nuclear receptor-interacting protein 1 repression 4 / Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / 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-4D8 / Nuclear receptor-interacting protein 1 / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.542 Å
AuthorsHuang, P. / Santori, F.R. / Littman, D.R. / Rastinejad, F.
CitationJournal: Cell Metab / Year: 2015
Title: Identification of Natural ROR gamma Ligands that Regulate the Development of Lymphoid Cells.
Authors: Santori, F.R. / Huang, P. / van de Pavert, S.A. / Douglass, E.F. / Leaver, D.J. / Haubrich, B.A. / Keber, R. / Lorbek, G. / Konijn, T. / Rosales, B.N. / Rozman, D. / Horvat, S. / Rahier, A. ...Authors: Santori, F.R. / Huang, P. / van de Pavert, S.A. / Douglass, E.F. / Leaver, D.J. / Haubrich, B.A. / Keber, R. / Lorbek, G. / Konijn, T. / Rosales, B.N. / Rozman, D. / Horvat, S. / Rahier, A. / Mebius, R.E. / Rastinejad, F. / Nes, W.D. / Littman, D.R.
History
DepositionJan 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear receptor ROR-gamma
C: Nuclear receptor-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7373
Polymers31,2942
Non-polymers4431
Water00
1
A: Nuclear receptor ROR-gamma
C: Nuclear receptor-interacting protein 1
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)190,42118
Polymers187,76512
Non-polymers2,6566
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_554-y,-x,-z-1/21
crystal symmetry operation11_654-x+y+1,y,-z-1/21
crystal symmetry operation12_544x,x-y-1,-z-1/21
Buried area14880 Å2
ΔGint-81 kcal/mol
Surface area65420 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-8 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.179, 158.179, 129.801
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Nuclear receptor ROR-gamma / Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / RAR-related orphan ...Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / RAR-related orphan receptor C / Retinoid-related orphan receptor-gamma


Mass: 29913.531 Da / Num. of mol.: 1 / Fragment: ligand-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1F3, RORC, RORG, RZRG / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P51449
#2: Protein/peptide Nuclear receptor-interacting protein 1 / Nuclear factor RIP140 / Receptor-interacting protein 140


Mass: 1380.632 Da / Num. of mol.: 1 / Fragment: LxxLL binding motif / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: P48552
#3: Chemical ChemComp-4D8 / (3beta,4alpha,5beta,14beta)-3-hydroxy-4-methylcholesta-8,24-diene-4-carboxylic acid / 4alpha-carboxy-4beta-methyl-zymosterol


Mass: 442.674 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H46O3

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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

Crystal growTemperature: 282 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.3M Potassium sodium tartrate, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 282K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2012
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.54→50 Å / Num. all: 12173 / Num. obs: 12173 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Net I/σ(I): 16

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.542→47.111 Å / SU ML: 0.32 / σ(F): 1.35 / Phase error: 19.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2193 567 4.71 %RANDOM
Rwork0.1867 ---
all0.1882 12156 --
obs0.1882 12041 99.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.542→47.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2075 0 32 0 2107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032156
X-RAY DIFFRACTIONf_angle_d0.7552912
X-RAY DIFFRACTIONf_dihedral_angle_d15.244817
X-RAY DIFFRACTIONf_chiral_restr0.048324
X-RAY DIFFRACTIONf_plane_restr0.002366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5418-3.89810.22841410.20562765X-RAY DIFFRACTION98
3.8981-4.46180.23091460.17382816X-RAY DIFFRACTION99
4.4618-5.61990.18571520.17072851X-RAY DIFFRACTION99
5.6199-47.11470.23641280.1983042X-RAY DIFFRACTION99
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)
13.21591.124-2.22821.7597-0.97442.52580.0961-0.11220.10560.30150.08550.43810.1623-0.28-0.12530.4956-0.06670.14070.47690.13530.506951.1448-45.2917-14.6793
22.32561.60161.24612.5738-0.66763.82990.0829-0.33140.20940.1524-0.2190.0306-0.22380.0637-0.41340.7155-0.14010.31130.98-0.08280.534353.8567-35.41632.4844
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain C

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