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- PDB-1hg4: Ultraspiracle ligand binding domain from Drosophila melanogaster -

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Basic information

Entry
Database: PDB / ID: 1hg4
TitleUltraspiracle ligand binding domain from Drosophila melanogaster
ComponentsULTRASPIRACLEEcdysone receptor
KeywordsNUCLEAR HORMONE RECEPTOR / TRANSCRIPTION FACTOR / LIGAND BINDING
Function / homology
Function and homology information


ecdysone biosynthetic process / cellular response to ecdysone / Regulation of pyruvate dehydrogenase (PDH) complex / Transcriptional regulation of white adipocyte differentiation / Regulation of lipid metabolism by PPARalpha / Signaling by Retinoic Acid / Transcriptional regulation of granulopoiesis / Cytoprotection by HMOX1 / ecdysone receptor holocomplex / activator ecdysone receptor complex ...ecdysone biosynthetic process / cellular response to ecdysone / Regulation of pyruvate dehydrogenase (PDH) complex / Transcriptional regulation of white adipocyte differentiation / Regulation of lipid metabolism by PPARalpha / Signaling by Retinoic Acid / Transcriptional regulation of granulopoiesis / Cytoprotection by HMOX1 / ecdysone receptor holocomplex / activator ecdysone receptor complex / Recycling of bile acids and salts / Carnitine metabolism / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Nuclear Receptor transcription pathway / response to ecdysone / pupariation / regulation of development, heterochronic / mushroom body development / metamorphosis / border follicle cell migration / polytene chromosome / hormone binding / regulation of organ growth / anatomical structure development / dendrite morphogenesis / neuron remodeling / nuclear steroid receptor activity / response to starvation / germ cell development / negative regulation of cell differentiation / core promoter sequence-specific DNA binding / nuclear receptor activity / cell differentiation / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / signaling receptor binding / negative regulation of DNA-templated transcription / dendrite / lipid binding / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus
Similarity search - Function
Retinoid X receptor/HNF4 / 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 ...Retinoid X receptor/HNF4 / 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-LPP / Protein ultraspiracle
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSchwabe, J.W.R. / Clayton, G.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: The Structure of the Ultraspiracle Ligand-Binding Domain Reveals a Nuclear Receptor Locked in an Inactive Conformation
Authors: Clayton, G.M. / Peak-Chew, S.Y. / Evans, R.M. / Schwabe, J.W.R.
History
DepositionDec 12, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2001Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 13, 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_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

Downloads & links

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Assembly

Deposited unit
A: ULTRASPIRACLE
B: ULTRASPIRACLE
C: ULTRASPIRACLE
D: ULTRASPIRACLE
E: ULTRASPIRACLE
F: ULTRASPIRACLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,02412
Polymers188,1316
Non-polymers3,8936
Water3,387188
1
A: ULTRASPIRACLE
C: ULTRASPIRACLE
D: ULTRASPIRACLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0126
Polymers94,0663
Non-polymers1,9473
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ULTRASPIRACLE
E: ULTRASPIRACLE
F: ULTRASPIRACLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0126
Polymers94,0663
Non-polymers1,9473
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)37.980, 86.190, 137.000
Angle α, β, γ (deg.)85.57, 85.94, 83.09
Int Tables number1
Space group name H-MP1
DetailsBUT THE BIOLOGICALLY ACTIVE MOLECULE IS HETERODIMER

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Components

#1: Protein
ULTRASPIRACLE / Ecdysone receptor


Mass: 31355.182 Da / Num. of mol.: 6 / Fragment: LIGAND-BINDING DOMAIN RESIDUES 230-508
Source method: isolated from a genetically manipulated source
Details: PHOSPHATIDIC ACID MODELLED IN LIGAND BINDING POCKET OF 6 PROTEIN MONOMERS
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20153
#2: Chemical
ChemComp-LPP / 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT / 3-SN-PHOSPHATIDIC ACID / 1,2-DIPALMITOYLDISODIUM SALT


Mass: 648.891 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C35H69O8P / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE C-TERMINAL STEROID-BINDING DOMAIN OF RECEPTOR FOR ECDYSONE. MAY PLAY AN IMPORTANT ROLE AS A ...THE C-TERMINAL STEROID-BINDING DOMAIN OF RECEPTOR FOR ECDYSONE. MAY PLAY AN IMPORTANT ROLE AS A MODULATOR IN INSECT METAMORPHOSIS. IMPORTANT IN EMBRYONIC AND POST-EMBRYONIC DEVELOPMENT. BINDS TO ECDYSONE RESPONSE ELEMENTS(ECRES). ONLY HETERODIMER OF USP AND ECR IS CAPABLE OF HIGH-AFFINITY BINDING TO ECDYSONE.

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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

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.77 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 4.6 / Method: vapor diffusion / Details: used streak-seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
2130 mMammonium sulfate1reservoir
3160 mMsodium acetate1reservoir
425 %PEG20001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.2→34 Å / Num. obs: 60384 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 4.4
Reflection
*PLUS
Lowest resolution: 34 Å / % possible obs: 90 % / Num. measured all: 175324
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.6 Å / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CNS1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ERE

1ere


Resolution: 2.4→34 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.284 3058 5 %RANDOM
Rwork0.248 ---
obs0.248 60384 90 %-
Refinement stepCycle: LAST / Resolution: 2.4→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11402 0 264 188 11854
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS

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