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- PDB-5m24: RARg mutant-S371E -

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Basic information

Entry
Database: PDB / ID: 5m24
TitleRARg mutant-S371E
ComponentsRetinoic acid receptor gamma
KeywordsNUCLEAR RECEPTOR
Function / homology
Function and homology information


growth plate cartilage chondrocyte growth / embryonic eye morphogenesis / embryonic hindlimb morphogenesis / Signaling by Retinoic Acid / positive regulation of programmed cell death / regulation of cell size / canonical Wnt signaling pathway / response to retinoic acid / nuclear retinoid X receptor binding / retinoic acid receptor signaling pathway ...growth plate cartilage chondrocyte growth / embryonic eye morphogenesis / embryonic hindlimb morphogenesis / Signaling by Retinoic Acid / positive regulation of programmed cell death / regulation of cell size / canonical Wnt signaling pathway / response to retinoic acid / nuclear retinoid X receptor binding / retinoic acid receptor signaling pathway / RNA polymerase II transcription regulator complex / Nuclear Receptor transcription pathway / nuclear receptor activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / sequence-specific double-stranded DNA binding / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / DNA-templated transcription / nucleoplasm / zinc ion binding / membrane / nucleus / cytoplasm
Similarity search - Function
: / : / Retinoic acid receptor / Retinoid X Receptor / Retinoid X Receptor / 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. ...: / : / Retinoic acid receptor / Retinoid X Receptor / Retinoid X Receptor / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(9cis)-retinoic acid / Retinoic acid receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsRochel, N. / Sirigu, S.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-09-BLAN-0127-01 France
INCAINCa-PL09-194 France
CitationJournal: PLoS ONE / Year: 2017
Title: Allosteric Regulation in the Ligand Binding Domain of Retinoic Acid Receptor gamma.
Authors: Chebaro, Y. / Sirigu, S. / Amal, I. / Lutzing, R. / Stote, R.H. / Rochette-Egly, C. / Rochel, N. / Dejaegere, A.
History
DepositionOct 11, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinoic acid receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1934
Polymers28,3461
Non-polymers8473
Water6,648369
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-4 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.871, 59.871, 157.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Retinoic acid receptor gamma / RAR-gamma / Nuclear receptor subfamily 1 group B member 3


Mass: 28346.008 Da / Num. of mol.: 1 / Fragment: UNP residues 178-423 / Mutation: S371E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RARG, NR1B3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P13631
#2: Chemical ChemComp-9CR / (9cis)-retinoic acid


Mass: 300.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O2
#3: Sugar ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Calcium Chloride, 0.1 M, Tris HCl pH 7.5, 14% Peg 6K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 32495 / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 70.17
Reflection shellResolution: 1.69→1.72 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 11.81 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LBD

3lbd


Resolution: 1.69→8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23361 1636 5.1 %RANDOM
Rwork0.19444 ---
obs0.19646 30570 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.546 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.36 Å2
Refinement stepCycle: 1 / Resolution: 1.69→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1861 0 58 372 2291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222016
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1182.042754
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.3645267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.08223.89677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66515374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3531515
X-RAY DIFFRACTIONr_chiral_restr0.0730.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021476
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1860.21109
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21424
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2262
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.245
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5011.51232
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.93922018
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4153784
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2724.5719
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.693→1.735 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 112 -
Rwork0.239 2080 -
obs--96.52 %

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