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- PDB-1pdu: Ligand-binding domain of Drosophila orphan nuclear receptor DHR38 -

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Basic information

Entry
Database: PDB / ID: 1pdu
TitleLigand-binding domain of Drosophila orphan nuclear receptor DHR38
Componentsnuclear hormone receptor HR38
KeywordsHORMONE/GROWTH FACTOR RECEPTOR / nuclear receptor / ligand-binding domain / HORMONE-GROWTH FACTOR RECEPTOR COMPLEX
Function / homology
Function and homology information


AKT phosphorylates targets in the nucleus / regulation of adult chitin-containing cuticle pigmentation / Nuclear Receptor transcription pathway / cuticle development / cellular response to corticotropin-releasing hormone stimulus / nuclear glucocorticoid receptor binding / core promoter sequence-specific DNA binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nuclear receptor activity / transcription regulator complex ...AKT phosphorylates targets in the nucleus / regulation of adult chitin-containing cuticle pigmentation / Nuclear Receptor transcription pathway / cuticle development / cellular response to corticotropin-releasing hormone stimulus / nuclear glucocorticoid receptor binding / core promoter sequence-specific DNA binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nuclear receptor activity / transcription regulator complex / sequence-specific DNA binding / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / signaling receptor binding / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
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 ...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
Probable nuclear hormone receptor HR38
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsBaker, K.D. / Shewchuk, L.M. / Korlova, T. / Makishima, M. / Hassell, A.M. / Wisely, B. / Caravella, J.A. / Lambert, M.H. / Wilson, T.M. / Mangelsdorf, D.J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: The Drosophila orphan nuclear receptor DHR38 mediates an atypical ecdysteroid signaling pathway.
Authors: Baker, K.D. / Shewchuk, L.M. / Korlova, T. / Makishima, M. / Hassell, A.M. / Wisely, B. / Caravella, J.A. / Lambert, M.H. / Reinking, J.L. / Krause, H. / Thummel, C.S. / Wilson, T.M. / Mangelsdorf, D.J.
History
DepositionMay 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: nuclear hormone receptor HR38
B: nuclear hormone receptor HR38


Theoretical massNumber of molelcules
Total (without water)56,3592
Polymers56,3592
Non-polymers00
Water3,081171
1
A: nuclear hormone receptor HR38


Theoretical massNumber of molelcules
Total (without water)28,1791
Polymers28,1791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: nuclear hormone receptor HR38


Theoretical massNumber of molelcules
Total (without water)28,1791
Polymers28,1791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.379, 82.231, 84.147
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein nuclear hormone receptor HR38 / dHR38


Mass: 28179.465 Da / Num. of mol.: 2 / Fragment: N-terminal, ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: HR38 / Plasmid: pRSETA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P49869
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.4 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 1.5 M Lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12-4 mg/mlprotein1drop
210 mMTris-HCl1droppH8.0
3500 mM1dropNaCl
41 mMEDTA1drop
55 mMdithiothreitol1drop
61 mMnervonic acid1drop
70.1 MHEPES1reservoirpH7.5
81.5 Mlithium sulfate1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9792, 0.9742, 0.9840
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 22, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97421
30.9841
ReflectionResolution: 2.3→20 Å / Num. all: 24797 / Num. obs: 23421 / % possible obs: 94.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.066
Reflection shellResolution: 2.3→2.44 Å / Num. unique all: 3013 / % possible all: 82.6
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 189296 / Rmerge(I) obs: 0.075

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Isotropic thermal model: anisotropic, / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 2342 -Random
Rwork0.21 ---
all-24797 --
obs-23421 94.6 %-
Displacement parametersBiso mean: 38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3632 0 0 171 3803
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0071
X-RAY DIFFRACTIONc_angle_d1.11
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 2.3→2.44 Å /
Num. reflection% reflection
Rfree343 -
obs3013 82.6 %
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.11
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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