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- PDB-4ozr: Crystal structure of the ligand binding domains of the Bovicola o... -

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Basic information

Entry
Database: PDB / ID: 4ozr
TitleCrystal structure of the ligand binding domains of the Bovicola ovis ecdysone receptor EcR/USP heterodimer (methylene lactam crystal)
Components
  • Ecdysone receptor
  • Retinoid X receptor
KeywordsTRANSCRIPTION / Ecdysone receptor / USP / methylene lactam / heterodimer / ligand binding domain
Function / homology
Function and homology information


ecdysone binding / ecdysone receptor signaling pathway / nuclear steroid receptor activity / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific DNA binding / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II ...ecdysone binding / ecdysone receptor signaling pathway / nuclear steroid receptor activity / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific DNA binding / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / 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 ...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 / Double treble clef zinc finger, C4 type / 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
Nuclear receptor subfamily 2 group B member 4 / Ecdysone receptor
Similarity search - Component
Biological speciesPediculus humanus subsp. corporis (human body louse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRen, B. / Peat, T.S. / Streltsov, V.A. / Pollard, M. / Fernley, R. / Grusovin, J. / Seabrook, S. / Pilling, P. / Phan, T. / Lu, L. ...Ren, B. / Peat, T.S. / Streltsov, V.A. / Pollard, M. / Fernley, R. / Grusovin, J. / Seabrook, S. / Pilling, P. / Phan, T. / Lu, L. / Lovrecz, G.O. / Graham, L.D. / Hill, R.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Unprecedented conformational flexibility revealed in the ligand-binding domains of the Bovicola ovis ecdysone receptor (EcR) and ultraspiracle (USP) subunits.
Authors: Ren, B. / Peat, T.S. / Streltsov, V.A. / Pollard, M. / Fernley, R. / Grusovin, J. / Seabrook, S. / Pilling, P. / Phan, T. / Lu, L. / Lovrecz, G.O. / Graham, L.D. / Hill, R.J.
History
DepositionFeb 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_symm_contact / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Ecdysone receptor
U: Retinoid X receptor


Theoretical massNumber of molelcules
Total (without water)45,0102
Polymers45,0102
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-6 kcal/mol
Surface area21480 Å2
MethodPISA
2
E: Ecdysone receptor
U: Retinoid X receptor

E: Ecdysone receptor
U: Retinoid X receptor


Theoretical massNumber of molelcules
Total (without water)90,0214
Polymers90,0214
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area8550 Å2
ΔGint-39 kcal/mol
Surface area38650 Å2
MethodPISA
3
E: Ecdysone receptor

U: Retinoid X receptor


Theoretical massNumber of molelcules
Total (without water)45,0102
Polymers45,0102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2080 Å2
ΔGint-14 kcal/mol
Surface area21520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.671, 42.430, 86.669
Angle α, β, γ (deg.)90.00, 117.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ecdysone receptor


Mass: 22935.762 Da / Num. of mol.: 1 / Fragment: UNP residues 281-514
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pediculus humanus subsp. corporis (human body louse)
Gene: Phum_PHUM467460 / Production host: Escherichia coli (E. coli) / References: UniProt: E0VVT4
#2: Protein Retinoid X receptor


Mass: 22074.666 Da / Num. of mol.: 1 / Fragment: UNP residues 222-415
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pediculus humanus subsp. corporis (human body louse)
Gene: Phum_PHUM164330 / Production host: Escherichia coli (E. coli) / References: UniProt: E0VFQ5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50 mM Tris pH 7.5, 150 mM NaCl, 5% glycerol, 5 mM DTT, 0.02% azide, 0.37 mM methylene lactam
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.7→69.3 Å / Num. obs: 13311 / % possible obs: 96.2 % / Redundancy: 2.5 % / Net I/σ(I): 9.1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→68.03 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2585 678 5.1 %
Rwork0.2239 --
obs0.2256 13290 95.25 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→68.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3099 0 0 91 3190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043179
X-RAY DIFFRACTIONf_angle_d1.1344304
X-RAY DIFFRACTIONf_dihedral_angle_d15.971199
X-RAY DIFFRACTIONf_chiral_restr0.076504
X-RAY DIFFRACTIONf_plane_restr0.006549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.90850.33461380.26312524X-RAY DIFFRACTION97
2.9085-3.20120.32791320.25242544X-RAY DIFFRACTION97
3.2012-3.66440.26671430.22472506X-RAY DIFFRACTION96
3.6644-4.61660.21171200.18692528X-RAY DIFFRACTION95
4.6166-68.05190.24711450.2352510X-RAY DIFFRACTION92
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)
16.7659-0.37242.72875.99230.94326.27050.35740.8187-0.2194-0.8938-0.3718-0.49960.81640.55180.33560.4470.00240.16270.37750.02930.29431.9787-10.08514.9693
20.4023-0.6216-1.75366.52444.36937.125-0.13781.50951.2337-1.5448-0.36430.665-2.2963-1.15121.11021.09330.1095-0.08521.26270.27280.954-15.0576.79521.2168
36.0180.08442.35428.7073-2.61316.1064-0.7884-0.24651.3866-0.601-0.62760.7353-0.5609-0.25271.40440.95030.0513-0.33320.78460.09430.9969-22.050412.8579.8806
45.2012-1.4580.56495.6507-0.6136.68590.15190.53640.77070.0237-0.20250.0171-0.4819-0.51050.04590.23690.04230.00690.50090.04260.3102-11.07540.880213.0259
55.6565-0.2365-0.05284.6380.83955.34760.0250.17310.29310.160.2252-0.1988-0.29360.1651-0.0920.28790.0154-0.01880.3470.05740.1645-0.9459-3.62617.3538
63.0970.2234-0.83721.4611.17291.2671-0.63731.0326-1.11280.24990.6779-0.13590.98210.8521-0.4910.8914-0.1374-0.29320.6836-0.05870.743215.9427-3.197514.9111
74.0992-1.59830.8491.47710.50821.53460.10780.51960.59060.156-0.0803-0.143-0.6511-0.7398-0.05140.42880.10660.03380.50760.13160.3155-12.21316.726923.4812
83.71960.5181-0.83532.8422-1.53583.58630.2646-1.0932-0.20090.3458-0.3418-0.0388-0.00490.27910.27540.2172-0.01720.00740.4224-0.02910.36245.41744.699950.067
95.07971.58020.02143.20270.52413.34250.1138-0.5148-0.22820.7445-0.03020.4076-0.0263-0.4534-0.06440.3113-0.01930.080.39350.06310.3319-3.5034-2.230944.6044
103.2926-0.2463-0.14961.65550.1573.46750.0573-0.04480.0352-0.176-0.01940.08210.0689-0.0318-0.02050.2001-0.0408-0.01860.1901-0.0060.24165.0843-2.896333.3832
114.559-3.736-2.10965.83450.29982.5047-0.2323-0.0347-0.89660.25560.1421.14270.05370.00480.11240.189-0.0168-0.02940.2859-0.02250.37942.2243-8.571329.4643
121.298-0.045-1.25062.7551.56658.0306-0.1706-0.66640.00810.7559-0.6342-0.4965-1.61580.26060.14540.3742-0.0677-0.05211.10560.03680.5267-13.7865-0.896355.7526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resid 282 through 301 )
2X-RAY DIFFRACTION2chain 'E' and (resid 302 through 328 )
3X-RAY DIFFRACTION3chain 'E' and (resid 329 through 334 )
4X-RAY DIFFRACTION4chain 'E' and (resid 335 through 409 )
5X-RAY DIFFRACTION5chain 'E' and (resid 410 through 467 )
6X-RAY DIFFRACTION6chain 'E' and (resid 468 through 475 )
7X-RAY DIFFRACTION7chain 'E' and (resid 476 through 509 )
8X-RAY DIFFRACTION8chain 'U' and (resid 194 through 226 )
9X-RAY DIFFRACTION9chain 'U' and (resid 227 through 273 )
10X-RAY DIFFRACTION10chain 'U' and (resid 274 through 339 )
11X-RAY DIFFRACTION11chain 'U' and (resid 340 through 364 )
12X-RAY DIFFRACTION12chain 'U' and (resid 365 through 389 )

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