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- PDB-1t76: Crystal structure of the androgen receptor ligand binding domain ... -

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Basic information

Entry
Database: PDB / ID: 1t76
TitleCrystal structure of the androgen receptor ligand binding domain in complex with a WxxVW motif
Components
  • Androgen receptor
  • WxxVW motif peptide
KeywordsHORMONE/GROWTH FACTOR RECEPTOR / nuclear receptor / transcription factor / ligand binding domain / AF-2 / androgen / testosterone / DHT / alpha-helical sandwich / HORMONE-GROWTH FACTOR RECEPTOR COMPLEX
Function / homology
Function and homology information


negative regulation of integrin biosynthetic process / intracellular receptor signaling pathway / androgen binding / androgen receptor signaling pathway / regulation of protein localization to plasma membrane / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of phosphorylation / steroid binding / negative regulation of extrinsic apoptotic signaling pathway ...negative regulation of integrin biosynthetic process / intracellular receptor signaling pathway / androgen binding / androgen receptor signaling pathway / regulation of protein localization to plasma membrane / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of phosphorylation / steroid binding / negative regulation of extrinsic apoptotic signaling pathway / beta-catenin binding / male gonad development / nuclear receptor activity / positive regulation of NF-kappaB transcription factor activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / positive regulation of cell population proliferation / positive regulation of gene expression / chromatin / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Androgen receptor / Androgen receptor / : / Retinoid X Receptor / Retinoid X 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 ...Androgen receptor / Androgen receptor / : / Retinoid X Receptor / Retinoid X 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
5-ALPHA-DIHYDROTESTOSTERONE / Androgen receptor
Similarity search - Component
Biological speciesPan troglodytes (chimpanzee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHur, E. / Pfaff, S.J. / Payne, E.S. / Gron, H. / Buehrer, B.M. / Fletterick, R.J.
CitationJournal: Plos Biol. / Year: 2004
Title: Recognition and accommodation at the androgen receptor coactivator binding interface.
Authors: Hur, E. / Pfaff, S.J. / Payne, E.S. / Gron, H. / Buehrer, B.M. / Fletterick, R.J.
History
DepositionMay 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Androgen receptor
B: WxxVW motif peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1876
Polymers32,7162
Non-polymers4724
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-33 kcal/mol
Surface area12160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.386, 66.420, 70.606
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Androgen receptor / Dihydrotestosterone receptor


Mass: 30877.957 Da / Num. of mol.: 1 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pan troglodytes (chimpanzee) / Gene: AR, NR3C4 / Production host: Escherichia coli (E. coli) / References: UniProt: O97775
#2: Protein/peptide WxxVW motif peptide


Mass: 1837.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Derived from phage display selections

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Non-polymers , 5 types, 92 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-DHT / 5-ALPHA-DIHYDROTESTOSTERONE


Mass: 290.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30O2 / Comment: hormone*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 1.9 Å3/Da / Density % sol: 35.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium citrate, HEPES, ethylene glycol, lithium sulfate, glycerol, TCEP, n-octyl glucoside, 5-alpha dihydrotestosterone, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.93221 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 12, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93221 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 15724 / Num. obs: 15724 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.9 Å2 / Rsym value: 0.067 / Net I/σ(I): 26.2
Reflection shellResolution: 2.1→2.14 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.563 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1211130.75 / 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
Rfree0.239 753 5 %RANDOM
Rwork0.208 ---
all-15170 --
obs-15170 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.0933 Å2 / ksol: 0.367382 e/Å3
Displacement parametersBiso mean: 43.8 Å2
Baniso -1Baniso -2Baniso -3
1-19.19 Å20 Å20 Å2
2---11.43 Å20 Å2
3----7.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2117 0 31 88 2236
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d17.979
X-RAY DIFFRACTIONc_improper_angle_d0.727
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.172
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.112.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.384 138 5.6 %
Rwork0.314 2343 -
obs-2481 99.9 %
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_LIGAND.PARDHT_LIGAND.TOP

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