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- PDB-23vy: Crystal structure of the mouse RORalpha ligand binding domain in ... -

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Basic information

Entry
Database: PDB / ID: 23vy
TitleCrystal structure of the mouse RORalpha ligand binding domain in fusion with an NRIP1 LXXLL peptide
ComponentsNuclear receptor ROR-alpha,undecapeptide
KeywordsTRANSCRIPTION / nuclear receptor / ligand binding domain / cholesterol / transcription factor
Function / homology
Function and homology information


SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / cGMP metabolic process / cerebellar Purkinje cell differentiation / cerebellar granule cell precursor proliferation / T-helper 17 cell differentiation / cellular response to sterol / regulation of steroid metabolic process / ligand-modulated transcription factor activity / positive regulation of circadian rhythm ...SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / cGMP metabolic process / cerebellar Purkinje cell differentiation / cerebellar granule cell precursor proliferation / T-helper 17 cell differentiation / cellular response to sterol / regulation of steroid metabolic process / ligand-modulated transcription factor activity / positive regulation of circadian rhythm / oxysterol binding / regulation of smoothened signaling pathway / muscle cell differentiation / triglyceride homeostasis / negative regulation of fat cell differentiation / regulation of macrophage activation / regulation of glucose metabolic process / positive regulation of vascular endothelial growth factor production / cellular response to interleukin-1 / intracellular receptor signaling pathway / nitric oxide biosynthetic process / xenobiotic metabolic process / cholesterol homeostasis / transcription corepressor binding / negative regulation of canonical NF-kappaB signal transduction / transcription coregulator binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / regulation of circadian rhythm / beta-catenin binding / negative regulation of inflammatory response / transcription coactivator binding / nuclear receptor activity / cellular response to tumor necrosis factor / angiogenesis / cellular response to hypoxia / sequence-specific DNA 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 / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / 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 ...Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / 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
CHOLESTEROL / Nuclear receptor ROR-alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLi, X. / Im, Y.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2023-00221356 Korea, Republic Of
CitationJournal: To Be Published
Title: Structure of a chimeric RORalpha ligand-binding domain in fusion with a RIP-140 coactivator peptide
Authors: Li, X. / Im, Y.J.
History
DepositionFeb 21, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear receptor ROR-alpha,undecapeptide
B: Nuclear receptor ROR-alpha,undecapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8744
Polymers61,1012
Non-polymers7732
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-6 kcal/mol
Surface area22410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.804, 75.775, 81.661
Angle α, β, γ (deg.)90.000, 119.040, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Nuclear receptor ROR-alpha,undecapeptide / Nuclear receptor RZR-alpha / Nuclear receptor subfamily 1 group F member 1 / RAR-related orphan ...Nuclear receptor RZR-alpha / Nuclear receptor subfamily 1 group F member 1 / RAR-related orphan receptor A / Retinoid-related orphan receptor-alpha


Mass: 30550.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The N-terminal Hexahistidine-tag and thrombin protease cleavage site are fused to the RORa LBD. The C-terminal residue 514 of the RORa LBD is fused to an undecapeptide, TLLQLLLGHKN, of NRIP1 ...Details: The N-terminal Hexahistidine-tag and thrombin protease cleavage site are fused to the RORa LBD. The C-terminal residue 514 of the RORa LBD is fused to an undecapeptide, TLLQLLLGHKN, of NRIP1 via a dipeptide, GG, linker.
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) synthetic construct (others)
Gene: Rora, Nr1f1, Rzra / Plasmid: pHIS2-Thr
Details (production host): The N-terminal Hexahistidine-tag cleavable by thrombin protease
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P51448
#2: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M HEPES-NaOH pH 9.0, 0.2M tri-sodium citrate, 5% propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 16980 / % possible obs: 99.7 % / Redundancy: 4 % / Biso Wilson estimate: 61.12 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 30.7
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 0.381 / Num. unique obs: 852

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Coot0.9.8.1model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→34.2 Å / SU ML: 0.3696 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.2212
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.249 1696 10 %
Rwork0.1814 15271 -
obs0.1882 16967 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.4 Å2
Refinement stepCycle: LAST / Resolution: 2.7→34.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4208 0 56 6 4270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914350
X-RAY DIFFRACTIONf_angle_d1.0565867
X-RAY DIFFRACTIONf_chiral_restr0.0492663
X-RAY DIFFRACTIONf_plane_restr0.009730
X-RAY DIFFRACTIONf_dihedral_angle_d19.18681625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.780.3811370.29431225X-RAY DIFFRACTION96.05
2.78-2.870.30821400.25621272X-RAY DIFFRACTION99.86
2.87-2.970.29491400.22811258X-RAY DIFFRACTION99.79
2.97-3.090.31171410.22261270X-RAY DIFFRACTION99.93
3.09-3.230.30661400.22341265X-RAY DIFFRACTION99.79
3.23-3.40.28581430.19871284X-RAY DIFFRACTION99.93
3.4-3.620.23781420.18871276X-RAY DIFFRACTION99.79
3.62-3.90.24391410.17921285X-RAY DIFFRACTION99.93
3.9-4.290.22891420.16371272X-RAY DIFFRACTION99.79
4.29-4.90.22261420.1521273X-RAY DIFFRACTION99.58
4.91-6.170.23681420.18751281X-RAY DIFFRACTION99.3
6.18-34.20.21861460.14911310X-RAY DIFFRACTION98.85

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