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- PDB-2r40: Crystal structure of 20E bound EcR/USP -

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Basic information

Entry
Database: PDB / ID: 2r40
TitleCrystal structure of 20E bound EcR/USP
Components
  • Ecdysone Receptor
  • Ultraspiracle
KeywordsGENE REGULATION / nuclear receptor ligand-binding domain / anti-parallel alpha-helical sandwich / ecdysone receptor / EcR
Function / homology
Function and homology information


ecdysone binding / ecdysone receptor signaling pathway / bile acid signaling pathway / nuclear steroid receptor activity / negative regulation of inflammatory response / nuclear receptor activity / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II ...ecdysone binding / ecdysone receptor signaling pathway / bile acid signaling pathway / nuclear steroid receptor activity / negative regulation of inflammatory response / nuclear receptor activity / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / 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
Chem-20E / Chem-EPH / CITRATE ANION / Ecdysone receptor / Gene regulation protein
Similarity search - Component
Biological speciesHeliothis virescens (tobacco budworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.402 Å
AuthorsMoras, D. / Billas, I.M.L. / Browning, C.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Critical Role of Desolvation in the Binding of 20-Hydroxyecdysone to the Ecdysone Receptor
Authors: Browning, C. / Martin, E. / Loch, C. / Wurtz, J.M. / Moras, D. / Stote, R.H. / Dejaegere, A.P. / Billas, I.M.L.
History
DepositionAug 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE THE SEQUENCE OF CHAIN D IN THIS STRUCTURE IS CORRECT BASED ON THE DIRECT SEQUENCING

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Ecdysone Receptor
A: Ultraspiracle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8897
Polymers60,3212
Non-polymers1,5685
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Ecdysone Receptor
A: Ultraspiracle
hetero molecules

D: Ecdysone Receptor
A: Ultraspiracle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,77714
Polymers120,6414
Non-polymers3,13610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area6630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.001, 58.001, 303.592
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 2 types, 2 molecules DA

#1: Protein Ecdysone Receptor / Ecdysteroid receptor / 20-hydroxy-ecdysone receptor / 20E receptor / EcRH / HvEcR


Mass: 30368.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heliothis virescens (tobacco budworm) / Gene: EcR / Plasmid: pET32b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O18473
#2: Protein Ultraspiracle / Gene regulation protein


Mass: 29951.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heliothis virescens (tobacco budworm) / Plasmid: pACYC11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7SIF6

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Non-polymers , 6 types, 90 molecules

#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-20E / (2beta,3beta,5beta,22R)-2,3,14,20,22,25-hexahydroxycholest-7-en-6-one / 2-beta,3-beta,14,20,22,25-Hexahydroxy-5-beta-cholet-7-en-6- one


Mass: 480.634 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O7 / Comment: hormone*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-EPH / L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE


Mass: 709.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H68NO8P / Comment: phospholipid*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.402→33.73 Å / Num. all: 24092

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
AMoREphasing
RefinementResolution: 2.402→33.73 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.893 / SU B: 16.621 / SU ML: 0.204 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.468 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.282 2391 9.9 %RANDOM
Rwork0.224 ---
all0.23 24087 --
obs0.23 24087 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.164 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.402→33.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3781 0 107 85 3973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223985
X-RAY DIFFRACTIONr_angle_refined_deg1.2892.0065390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7955473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17423.486175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.70415722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4151534
X-RAY DIFFRACTIONr_chiral_restr0.0870.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022906
X-RAY DIFFRACTIONr_nbd_refined0.2060.21937
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22759
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2111
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0570.22
X-RAY DIFFRACTIONr_mcbond_it0.5651.52461
X-RAY DIFFRACTIONr_mcangle_it0.93723853
X-RAY DIFFRACTIONr_scbond_it1.32131719
X-RAY DIFFRACTIONr_scangle_it2.0664.51537
LS refinement shellResolution: 2.402→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 164 -
Rwork0.247 1521 -
all-1685 -
obs--98.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5853-0.28050.32894.2343-2.21954.7428-0.03360.1507-0.0832-0.27470.03610.07960.2763-0.1911-0.0025-0.01510.02640.016-0.2695-0.0093-0.243222.5393-12.31-36.9447
22.12570.5790.02153.08690.76494.320.1786-0.1198-0.05790.2553-0.1915-0.28530.1360.24090.0129-0.03860.0059-0.0741-0.29560.1124-0.138731.8657-11.7995-11.0578
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A206 - 455
2X-RAY DIFFRACTION2D287 - 529

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