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- PDB-1exx: ENANTIOMER DISCRIMINATION ILLUSTRATED BY CRYSTAL STRUCTURES OF TH... -

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Basic information

Entry
Database: PDB / ID: 1exx
TitleENANTIOMER DISCRIMINATION ILLUSTRATED BY CRYSTAL STRUCTURES OF THE HUMAN RETINOIC ACID RECEPTOR HRARGAMMA LIGAND BINDING DOMAIN: THE COMPLEX WITH THE INACTIVE S-ENANTIOMER BMS270395.
ComponentsRETINOIC ACID RECEPTOR GAMMA-2
KeywordsGENE REGULATION / enantiomer discrimination / retinoid ligand complexes / antiparallel alpha-helical sandwich fold / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


Harderian gland development / regulation of myeloid cell differentiation / growth plate cartilage chondrocyte growth / trachea cartilage development / embryonic eye morphogenesis / embryonic camera-type eye development / glandular epithelial cell development / prostate gland epithelium morphogenesis / positive regulation of programmed cell death / negative regulation of chondrocyte differentiation ...Harderian gland development / regulation of myeloid cell differentiation / growth plate cartilage chondrocyte growth / trachea cartilage development / embryonic eye morphogenesis / embryonic camera-type eye development / glandular epithelial cell development / prostate gland epithelium morphogenesis / positive regulation of programmed cell death / negative regulation of chondrocyte differentiation / embryonic hindlimb morphogenesis / anterior/posterior pattern specification / Signaling by Retinoic Acid / regulation of myelination / regulation of cell size / face development / canonical Wnt signaling pathway / retinoic acid receptor signaling pathway / nuclear retinoid X receptor binding / response to retinoic acid / negative regulation of stem cell proliferation / cellular response to retinoic acid / hormone-mediated signaling pathway / stem cell proliferation / cellular response to leukemia inhibitory factor / neural tube closure / multicellular organism growth / Nuclear Receptor transcription pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear receptor activity / sequence-specific double-stranded DNA binding / transcription regulator complex / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / chromatin binding / positive regulation of cell population proliferation / positive regulation of gene expression / chromatin / apoptotic process / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / 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 / Zinc finger, C4 type (two domains) / 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 / 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-961 / Retinoic acid receptor gamma / Retinoic acid receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.67 Å
AuthorsKlaholz, B.P. / Mitschler, A. / Belema, M. / Zusi, C. / Moras, D. / Structural Proteomics in Europe (SPINE)
Citation
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.
#1: 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.
#2: Journal: To be Published / Year: 2000
Title: Structural Basis for Isotype Selectivity of the Human Retinoic Acid Nuclear Receptor.
Authors: Klaholz, B.P. / Mitschler, A. / Moras, D.
History
DepositionMay 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 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: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: RETINOIC ACID RECEPTOR GAMMA-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8013
Polymers27,8901
Non-polymers9102
Water4,972276
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, 155.615
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-2


Mass: 27890.498 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: NUCLEUS / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / References: UniProt: P22932, UniProt: P13631*PLUS
#2: Chemical ChemComp-961 / 3-FLUORO-4-[2-HYDROXY-2-(5,5,8,8-TETRAMETHYL-5,6,7,8,-TETRAHYDRO-NAPHTALEN-2-YL)-ACETYLAMINO]-BENZOIC ACID / BMS961


Mass: 399.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H26FNO4
#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.: 276 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.550.73
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2901vapor diffusion, hanging drop7sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
2902vapor diffusion, hanging drop7sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃
Components of the solutions
*PLUS
Chemical formula: NaOAc

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID1310.6887
SYNCHROTRONESRF BM1420.9612
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEApr 27, 1998
MARRESEARCH2IMAGE PLATEOct 31, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.68871
20.96121
ReflectionResolution: 1.67→25 Å / Num. all: 33233 / Num. obs: 33233 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.97 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 33.1
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 4 % / Rmerge(I) obs: 0.315 / Num. unique all: 1608 / % possible all: 97.9
Reflection
*PLUS
Num. measured all: 165142 / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
% possible obs: 97.9 % / Mean I/σ(I) obs: 3.5 / Rmerge(I) obs: 0.315

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Processing

Software
NameClassification
SHELXL-97refinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.67→6 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.243 1617 random
Rwork0.179 --
all0.181 32478 -
obs0.181 30861 -
Refinement stepCycle: LAST / Resolution: 1.67→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 69 276 2237
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d2.16
X-RAY DIFFRACTIONs_torsion_impr_deg1.451
X-RAY DIFFRACTIONs_torsion_deg27.27
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg1.451
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg27.27

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