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- PDB-2nxx: Crystal Structure of the Ligand-Binding Domains of the T.castaneu... -

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Basic information

Entry
Database: PDB / ID: 2nxx
TitleCrystal Structure of the Ligand-Binding Domains of the T.castaneum (Coleoptera) Heterodimer EcrUSP Bound to Ponasterone A
Components
  • Ecdysone Receptor (EcR, NRH1)
  • Ultraspiracle (USP, NR2B4)
KeywordsHORMONE/GROWTH FACTOR / Hormone Receptor / apo and holo Ligand Binding Pocket / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


ecdysone binding / ecdysone receptor-mediated signaling pathway / nuclear steroid receptor activity / nuclear receptor activity / sequence-specific DNA binding / DNA-binding transcription factor activity / zinc ion binding / nucleus
Similarity search - Function
Ecdysteroid receptor / Ecdysone 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. ...Ecdysteroid receptor / Ecdysone 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
2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE / Ultraspiracle nuclear receptor / 20-hydroxy-ecdysone receptor
Similarity search - Component
Biological speciesTribolium castaneum (red flour beetle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsIwema, T. / Billas, I. / Moras, D.
CitationJournal: Embo J. / Year: 2007
Title: Structural and functional characterization of a novel type of ligand-independent RXR-USP receptor.
Authors: Iwema, T. / Billas, I.M. / Beck, Y. / Bonneton, F. / Nierengarten, H. / Chaumot, A. / Richards, G. / Laudet, V. / Moras, D.
History
DepositionNov 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999 SEQUENCE THE SEQUENCE OF BOTH ENTITIES WAS NOT AVAILABLE AT THE UNIPROT SEQUENCE DATABASE AT THE ... SEQUENCE THE SEQUENCE OF BOTH ENTITIES WAS NOT AVAILABLE AT THE UNIPROT SEQUENCE DATABASE AT THE TIME OF PROCESSING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ultraspiracle (USP, NR2B4)
E: Ecdysone Receptor (EcR, NRH1)
B: Ultraspiracle (USP, NR2B4)
F: Ecdysone Receptor (EcR, NRH1)
C: Ultraspiracle (USP, NR2B4)
G: Ecdysone Receptor (EcR, NRH1)
D: Ultraspiracle (USP, NR2B4)
H: Ecdysone Receptor (EcR, NRH1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,68312
Polymers221,8258
Non-polymers1,8594
Water4,810267
1
A: Ultraspiracle (USP, NR2B4)
E: Ecdysone Receptor (EcR, NRH1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9213
Polymers55,4562
Non-polymers4651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ultraspiracle (USP, NR2B4)
F: Ecdysone Receptor (EcR, NRH1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9213
Polymers55,4562
Non-polymers4651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ultraspiracle (USP, NR2B4)
G: Ecdysone Receptor (EcR, NRH1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9213
Polymers55,4562
Non-polymers4651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ultraspiracle (USP, NR2B4)
H: Ecdysone Receptor (EcR, NRH1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9213
Polymers55,4562
Non-polymers4651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.540, 89.628, 160.247
Angle α, β, γ (deg.)90.00, 91.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ultraspiracle (USP, NR2B4)


Mass: 26576.934 Da / Num. of mol.: 4 / Fragment: Ligand Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tribolium castaneum (red flour beetle) / Strain: San Bernardino / Gene: Ultraspiracle (USP) / Plasmid: pACYC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: A1JUG2
#2: Protein
Ecdysone Receptor (EcR, NRH1)


Mass: 28879.270 Da / Num. of mol.: 4 / Fragment: Ligand Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tribolium castaneum (red flour beetle) / Strain: San Bernardino / Gene: Ecdysone Receptor (EcR) / Plasmid: pHGWA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: A1JUG3
#3: 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.: 4 / Source method: obtained synthetically / Formula: C27H44O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 6% PEG 4000, 50 mM Pipes (pH=6.5), 50 mM NaCl, 10 mM Hepes (pH=7.5), 2 mM TCEP against a reservoir containing 12% PEG 4000, 100 mM Pipes (pH=6.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 17, 2005
RadiationMonochromator: Sagitally focusing Ge(220) and a multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 57329 / Num. obs: 56221 / % possible obs: 98.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 60.6 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 7.8
Reflection shellResolution: 2.75→2.85 Å / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 3.4 / Num. unique all: 5654 / Rsym value: 0.238 / % possible all: 95

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PonA-bound HvEcR/HsRXRa (no H12), BtEcR/BtUSP (no H12)

Resolution: 2.75→50 Å / FOM work R set: 0.765 / Cross valid method: Free R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.281 2841 5 %Random
Rwork0.249 ---
all0.249 56221 --
obs0.249 56221 98.1 %-
Solvent computationBsol: 47.594 Å2
Displacement parametersBiso mean: 66.876 Å2
Baniso -1Baniso -2Baniso -3
1-7.847 Å20 Å2-1.635 Å2
2---3.615 Å20 Å2
3----4.233 Å2
Refinement stepCycle: LAST / Resolution: 2.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14842 0 132 267 15241
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.568
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.75-2.770.425590.39410201079
2.77-2.790.449590.3810071066
2.79-2.810.375440.35510111055
2.81-2.830.357540.34110441098
2.83-2.850.38450.3210281073
2.85-2.870.507530.33111021155
2.87-2.890.297510.32210151066
2.89-2.910.384450.31810141059
2.91-2.940.407480.34110291077
2.94-2.960.347620.31910931155
2.96-2.990.382500.32810361086
2.99-3.010.341580.32610141072
3.01-3.040.322450.30210831128
3.04-3.070.323550.33110411096
3.07-3.10.393510.32211001151
3.1-3.130.354560.32910481104
3.13-3.160.39610.31510461107
3.16-3.190.328620.3110931155
3.19-3.220.302480.28910601108
3.22-3.260.321530.29410971150
3.26-3.30.35670.30910551122
3.3-3.340.355660.30310651131
3.34-3.380.389660.28810641130
3.38-3.420.322730.28910491122
3.42-3.460.35600.27310621122
3.46-3.510.293570.29110921149
3.51-3.560.374540.27510741128
3.56-3.620.255580.27610711129
3.62-3.670.346600.30110721132
3.67-3.730.306660.29210911157
3.73-3.80.309570.24910401097
3.8-3.870.294630.25111021165
3.87-3.940.273500.24410711121
3.94-4.020.31600.2510651125
4.02-4.110.196460.2311211167
4.11-4.20.247610.23210531114
4.2-4.310.261620.22710951157
4.31-4.420.251610.21610691130
4.42-4.550.235680.20611051173
4.55-4.70.2480.19410861134
4.7-4.870.192500.19610941144
4.87-5.060.235600.20410591119
5.06-5.290.268680.21410991167
5.29-5.570.266580.24310991157
5.57-5.920.288610.26111041165
5.92-6.380.35580.26510731131
6.38-7.020.298490.2411121161
7.02-8.030.214580.17710831141
8.03-10.10.153650.13410891154
10.1-500.211520.20510851137
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2ponA.par
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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