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- PDB-1fcy: ISOTYPE SELECTIVITY OF THE HUMAN RETINOIC ACID NUCLEAR RECEPTOR H... -

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Basic information

Entry
Database: PDB / ID: 1fcy
TitleISOTYPE SELECTIVITY OF THE HUMAN RETINOIC ACID NUCLEAR RECEPTOR HRAR: THE COMPLEX WITH THE RARBETA/GAMMA-SELECTIVE RETINOID CD564
ComponentsRETINOIC ACID RECEPTOR GAMMA-1
KeywordsGENE REGULATION / isotype selectivity / retinoid ligand complexes / drug design / antiparallel alpha-helical sandwich fold / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


regulation of myeloid cell differentiation / Harderian gland development / trachea cartilage development / growth plate cartilage chondrocyte growth / glandular epithelial cell development / embryonic eye morphogenesis / embryonic camera-type eye development / prostate gland epithelium morphogenesis / negative regulation of chondrocyte differentiation / positive regulation of programmed cell death ...regulation of myeloid cell differentiation / Harderian gland development / trachea cartilage development / growth plate cartilage chondrocyte growth / glandular epithelial cell development / embryonic eye morphogenesis / embryonic camera-type eye development / prostate gland epithelium morphogenesis / negative regulation of chondrocyte differentiation / positive regulation of programmed cell death / embryonic hindlimb morphogenesis / anterior/posterior pattern specification / Signaling by Retinoic Acid / regulation of myelination / regulation of cell size / face development / canonical Wnt signaling pathway / response to retinoic acid / nuclear retinoid X receptor binding / negative regulation of stem cell proliferation / retinoic acid receptor signaling pathway / cellular response to retinoic acid / cellular response to leukemia inhibitory factor / stem cell proliferation / neural tube closure / Nuclear Receptor transcription pathway / multicellular organism growth / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear receptor activity / 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 / positive regulation of cell population proliferation / apoptotic process / chromatin binding / positive regulation of gene expression / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / membrane / 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
Chem-564 / Retinoic acid receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKlaholz, B.P. / Mitschler, A. / Moras, D. / Structural Proteomics in Europe (SPINE)
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Structural basis for isotype selectivity of the human retinoic acid nuclear receptor.
Authors: Klaholz, B.P. / Mitschler, A. / Moras, D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Enantiomer discrimination illustrated by high-resolution crystal structures of the human nuclear receptor hRARgamma.
Authors: Klaholz, B.P. / Mitschler, A. / Belema, M. / Zusi, C. / Moras, D.
#2: Journal: Nat.Struct.Biol. / Year: 1998
Title: Conformational adaptation of agonists to the human nuclear receptor hRARgamma.
Authors: Klaholz, B.P. / Renaud, J.-P. / Mitschler, A. / Zusi, C. / Chambon, P. / Gronemeyer, H. / Moras, D.
#3: Journal: Nature / Year: 1995
Title: Crystal structure of the RARgamma ligand-binding domain bound to all-trans retinoic acid.
Authors: Renaud, J.-P. / Rochel, N. / Ruff, M. / Vivat, V. / Chambon, P. / Gronemeyer, H. / Moras, D.
History
DepositionJul 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RETINOIC ACID RECEPTOR GAMMA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5033
Polymers26,6061
Non-polymers8972
Water5,531307
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.849, 59.849, 155.158
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

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Components

#1: Protein RETINOIC ACID RECEPTOR GAMMA-1 / RAR-GAMMA-1


Mass: 26606.148 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH CD564, RESIDUE 564 / Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / References: UniProt: P13631
#2: Chemical ChemComp-564 / 6-(5,5,8,8-TETRAMETHYL-5,6,7,8-TETRAHYDRO-NAPHTALENE-2-CARBONYL)-NAPHTALENE-2-CARBOXYLIC ACID / CD564


Mass: 386.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H26O3
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.25 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 MPIPES1reservoir
20.2-1.7 M1reservoirNaOAc
32-5 mg/mlprotein1drop
410 mMTris-HCl1drop
55 mM1,4-dithio-DL-threitol1drop
6500 mM1dropNaCl
70.15 mMn-dodecyl-alpha-D-maltoside1drop
82 mMCHAPS1drop
94 %glycerol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8345
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 6, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8345 Å / Relative weight: 1
ReflectionResolution: 1.3→18 Å / Num. all: 64898 / Num. obs: 64898 / % possible obs: 92.6 % / Redundancy: 3.55 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 40.7
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 3 / Num. unique all: 3026 / % possible all: 88.7
Reflection
*PLUS
Num. measured all: 230315
Reflection shell
*PLUS
% possible obs: 88.7 %

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Processing

Software
NameClassification
SHELXL-97refinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EXA

1exa


Resolution: 1.3→6 Å / Num. parameters: 20843 / Num. restraintsaints: 25637 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 2.5%
RfactorNum. reflection% reflectionSelection details
Rfree0.1641 3235 5.1 %random
Rwork0.1329 ---
all0.134 64056 --
obs0.1329 60821 92.5 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 23 / Occupancy sum hydrogen: 1940 / Occupancy sum non hydrogen: 2191.7
Refinement stepCycle: LAST / Resolution: 1.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 64 307 2313
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_torsion_impr_deg1.65
X-RAY DIFFRACTIONs_torsion_deg26.7
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0249
X-RAY DIFFRACTIONs_zero_chiral_vol0.072
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.083
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.022
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.038
X-RAY DIFFRACTIONs_approx_iso_adps0.09
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 6 Å / σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.133
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.4
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg26.7
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg1.65
X-RAY DIFFRACTIONs_plane_restr0.025
X-RAY DIFFRACTIONs_chiral_restr0.072
LS refinement shell
*PLUS
Rfactor obs: 0.206

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