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- PDB-2z4j: Crystal structure of AR LBD with SHP peptide NR Box 2 -

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Basic information

Entry
Database: PDB / ID: 2z4j
TitleCrystal structure of AR LBD with SHP peptide NR Box 2
Components
  • Androgen receptor
  • Nuclear receptor 0B2
KeywordsTRANSCRIPTION / Androgen receptor / ligand binding domain / SHP / Co-repressor
Function / homology
Function and homology information


POU domain binding / positive regulation of integrin biosynthetic process / cellular response to testosterone stimulus / androgen binding / androgen receptor signaling pathway / membraneless organelle assembly / RNA polymerase II general transcription initiation factor binding / peroxisome proliferator activated receptor binding / nuclear thyroid hormone receptor binding / cellular response to steroid hormone stimulus ...POU domain binding / positive regulation of integrin biosynthetic process / cellular response to testosterone stimulus / androgen binding / androgen receptor signaling pathway / membraneless organelle assembly / RNA polymerase II general transcription initiation factor binding / peroxisome proliferator activated receptor binding / nuclear thyroid hormone receptor binding / cellular response to steroid hormone stimulus / nuclear steroid receptor activity / RUNX2 regulates osteoblast differentiation / positive regulation of transcription by RNA polymerase III / animal organ regeneration / cellular response to estrogen stimulus / response to glucose / estrogen response element binding / cholesterol metabolic process / nuclear retinoid X receptor binding / estrogen receptor signaling pathway / transcription regulator inhibitor activity / RNA polymerase II core promoter sequence-specific DNA binding / regulation of protein localization to plasma membrane / intracellular receptor signaling pathway / steroid binding / male gonad development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / negative regulation of extrinsic apoptotic signaling pathway / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / circadian regulation of gene expression / positive regulation of insulin secretion / positive regulation of cell differentiation / circadian rhythm / molecular condensate scaffold activity / Nuclear Receptor transcription pathway / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / positive regulation of miRNA transcription / beta-catenin binding / nuclear receptor activity / transcription coactivator binding / transcription corepressor activity / cell-cell signaling / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / molecular adaptor activity / response to ethanol / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / transcription cis-regulatory region binding / Ub-specific processing proteases / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of gene expression / signaling receptor binding / protein domain specific binding / negative regulation of DNA-templated transcription / positive regulation of gene expression / positive regulation of cell population proliferation / chromatin binding / positive regulation of DNA-templated transcription / protein-containing complex binding / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / DNA-templated transcription / nucleoplasm / zinc ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Nuclear receptor subfamily 0 group B member 1/2 / Androgen receptor / Androgen receptor / : / 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 receptor subfamily 0 group B member 1/2 / Androgen receptor / Androgen receptor / : / 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
5-ALPHA-DIHYDROTESTOSTERONE / Androgen receptor / Nuclear receptor subfamily 0 group B member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJouravel, N. / Fletterick, R.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Interaction between the androgen receptor and a segment of its corepressor SHP
Authors: Jouravel, N. / Sablin, E. / Arnold, L.A. / Guy, R.K. / Fletterick, R.J.
History
DepositionJun 19, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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: Androgen receptor
B: Nuclear receptor 0B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3643
Polymers30,0732
Non-polymers2901
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.979, 66.542, 71.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Androgen receptor / Dihydrotestosterone receptor


Mass: 28917.945 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AR, NR3C4 / Plasmid: pETDuet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P10275
#2: Protein/peptide Nuclear receptor 0B2 / SHP NR BOX 2 / Orphan nuclear receptor SHP / Small heterodimer partner


Mass: 1155.470 Da / Num. of mol.: 1 / Fragment: residues 115-124 / Source method: obtained synthetically
Details: Synthetic peptide. This sequence occurs naturally in humans.
References: UniProt: Q15466
#3: Chemical ChemComp-DHT / 5-ALPHA-DIHYDROTESTOSTERONE


Mass: 290.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.22 Å3/Da / Density % sol: 44.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bis-Tris Propane, 1.2M Potassium Sodium Tartrate tetrahydrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11589 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 24, 2004
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11589 Å / Relative weight: 1
ReflectionResolution: 2.6→24.41 Å / Num. all: 8674 / Num. obs: 7836 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 29.9 Å2
Reflection shellHighest resolution: 2.6 Å / % possible all: 90.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T63

1t63


Resolution: 2.6→24.41 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 170678.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 415 5.3 %RANDOM
Rwork0.207 ---
obs0.207 7836 90.5 %-
all-8674 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.7276 Å2 / ksol: 0.341867 e/Å3
Displacement parametersBiso mean: 44.1 Å2
Baniso -1Baniso -2Baniso -3
1-13.58 Å20 Å20 Å2
2---11.67 Å20 Å2
3----1.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.6→24.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2110 0 21 6 2137
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
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_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it1.792
X-RAY DIFFRACTIONc_scangle_it2.712.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.33 69 6.2 %
Rwork0.326 1050 -
obs--78.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4DHT.paramDHT.top

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