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- PDB-1z5x: hemipteran ecdysone receptor ligand-binding domain complexed with... -

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Basic information

Entry
Database: PDB / ID: 1z5x
Titlehemipteran ecdysone receptor ligand-binding domain complexed with ponasterone A
Components
  • Ecdysone receptor ligand binding domain
  • Ultraspiracle protein (USP) a homologue of RXREcdysone receptor
KeywordsHormone/Growth Factor Receptor / ecdysone receptor / ponasterone A / nuclear receptor / ECR / USP / ecdysone / Hormone-Growth Factor Receptor COMPLEX
Function / homologyRetinoid X Receptor / Retinoid X Receptor / Orthogonal Bundle / Mainly Alpha / 2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE / PHOSPHATE ION
Function and homology information
Biological speciesBemisia tabaci (sweet potato whitefly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsCarmichael, J.A. / Lawrence, M.C. / Graham, L.D. / Pilling, P.A. / Epa, V.C. / Noyce, L. / Lovrecz, G. / Winkler, D.A. / Pawlak-Skrzecz, A.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The X-ray structure of a hemipteran ecdysone receptor ligand-binding domain: comparison with a lepidopteran ecdysone receptor ligand-binding domain and implications for insecticide design.
Authors: Carmichael, J.A. / Lawrence, M.C. / Graham, L.D. / Pilling, P.A. / Epa, V.C. / Noyce, L. / Lovrecz, G. / Winkler, D.A. / Pawlak-Skrzecz, A. / Eaton, R.E. / Hannan, G.N. / Hill, R.J.
History
DepositionMar 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
Remark 999SEQUENCE According to authors the N-termini of the crystal contents could not be verified. SDS-PAGE ...SEQUENCE According to authors the N-termini of the crystal contents could not be verified. SDS-PAGE analysis of crystals and stored protein revealed polypeptides of lower molecular weight than expected, presumably the result of progressive proteolysis. N-terminal sequencing of major bands extracted from SDS-PAGE could only confirm one band as corresponding to a sequence starting at residue LEU U 285. At the time of processing there were no suitable database references for chains U or E

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
U: Ultraspiracle protein (USP) a homologue of RXR
E: Ecdysone receptor ligand binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7157
Polymers65,8702
Non-polymers8455
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-28 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.005, 143.005, 84.015
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Detailsthe biological assembly is a heterodimer of Usp (chain U) and Ecr (chain E)

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Components

#1: Protein Ultraspiracle protein (USP) a homologue of RXR / Ecdysone receptor


Mass: 29997.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bemisia tabaci (sweet potato whitefly) / Gene: Usp / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi-5 (Invitrogen)
#2: Protein Ecdysone receptor ligand binding domain


Mass: 35873.070 Da / Num. of mol.: 1 / Fragment: ligand binding subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bemisia tabaci (sweet potato whitefly) / Gene: Ecr / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi-5 (Invitrogen)
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-P1A / 2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE / PONASTERONE A / 25-DEOXYECDYSTERONE / 25-DEOXY-20-HYDROXYECDYSONE,


Mass: 464.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O6

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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: 4.35 Å3/Da / Density % sol: 71.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 M ammonium phosphate, 4.5 % trehalose, 10 mM DTT, 10 % glycerol, 3 mM ponasterone A, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 21, 2002 / Details: Yale-MSC mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.07→27.48 Å / Num. all: 16756 / Num. obs: 16756 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Rsym value: 0.13 / Net I/σ(I): 19.3
Reflection shellResolution: 3.07→3.11 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 5.6 / Num. unique all: 2713 / Rsym value: 0.51 / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model derived from pdb entry 1DKF

1dkf


Resolution: 3.07→27.48 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2256128.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 843 5 %RANDOM
Rwork0.205 ---
all0.205 16740 --
obs0.205 16740 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.4674 Å2 / ksol: 0.364873 e/Å3
Displacement parametersBiso mean: 46.2 Å2
Baniso -1Baniso -2Baniso -3
1--9.41 Å20 Å20 Å2
2---9.41 Å20 Å2
3---18.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 3.07→27.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3473 0 53 0 3526
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.07
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
LS refinement shellResolution: 3.07→3.26 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.364 153 5.6 %
Rwork0.318 2560 -
obs-2713 99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PO4_XPLOR_PAR.TXTPONA.TOP
X-RAY DIFFRACTION3PONA.PARAMPO4_XPLOR_TOP.TXT

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