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- PDB-1r4i: Crystal Structure of Androgen Receptor DNA-Binding Domain Bound t... -

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Basic information

Entry
Database: PDB / ID: 1r4i
TitleCrystal Structure of Androgen Receptor DNA-Binding Domain Bound to a Direct Repeat Response Element
Components
  • 5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*CP*AP*AP*GP*AP*AP*CP*AP*G)-3'
  • 5'-D(*CP*TP*GP*TP*TP*CP*TP*TP*GP*AP*TP*GP*TP*TP*CP*TP*GP*G)-3'
  • Androgen receptor
KeywordsTRANSCRIPTION/DNA / AR / Steroid Receptor / Protein-DNA Complex / Androgen / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


reproductive behavior / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / copulation / male sex differentiation / skeletal muscle hypertrophy / regulation of prostatic bud formation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of penile erection / ribonucleotide binding / reproductive system development ...reproductive behavior / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / copulation / male sex differentiation / skeletal muscle hypertrophy / regulation of prostatic bud formation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of penile erection / ribonucleotide binding / reproductive system development / male courtship behavior / Ub-specific processing proteases / male somatic sex determination / activation of prostate induction by androgen receptor signaling pathway / lateral sprouting involved in mammary gland duct morphogenesis / SUMOylation of intracellular receptors / POU domain binding / negative regulation of integrin biosynthetic process / regulation of developmental growth / reproductive structure development / male genitalia morphogenesis / positive regulation of integrin biosynthetic process / Nuclear Receptor transcription pathway / tertiary branching involved in mammary gland duct morphogenesis / animal organ formation / cellular response to follicle-stimulating hormone stimulus / androgen binding / Leydig cell differentiation / regulation of systemic arterial blood pressure / epithelial cell morphogenesis / prostate gland growth / epithelial cell differentiation involved in prostate gland development / positive regulation of epithelial cell proliferation involved in prostate gland development / prostate gland epithelium morphogenesis / intracellular receptor signaling pathway / cellular response to testosterone stimulus / fertilization / RNA polymerase II general transcription initiation factor binding / positive regulation of insulin-like growth factor receptor signaling pathway / positive regulation of transcription by RNA polymerase III / positive regulation of intracellular estrogen receptor signaling pathway / nuclear androgen receptor binding / cellular response to steroid hormone stimulus / morphogenesis of an epithelial fold / response to testosterone / seminiferous tubule development / androgen receptor signaling pathway / single fertilization / mammary gland alveolus development / regulation of protein localization to plasma membrane / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of phosphorylation / steroid binding / insulin-like growth factor receptor signaling pathway / epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of cell differentiation / response to insulin / multicellular organism growth / beta-catenin binding / transcription coactivator binding / positive regulation of miRNA transcription / nuclear receptor activity / negative regulation of epithelial cell proliferation / male gonad development / MAPK cascade / response to estradiol / positive regulation of NF-kappaB transcription factor activity / ATPase binding / spermatogenesis / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / positive regulation of MAPK cascade / molecular adaptor activity / transcription cis-regulatory region binding / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / protein domain specific binding / axon / signaling receptor binding / negative regulation of DNA-templated transcription / chromatin binding / dendrite / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II
Similarity search - Function
Androgen receptor / Androgen receptor / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / 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 ...Androgen receptor / Androgen receptor / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Androgen receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsShaffer, P.L. / Jivan, A. / Dollins, D.E. / Claessens, F. / Gewirth, D.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structural basis of androgen receptor binding to selective androgen response elements.
Authors: Shaffer, P.L. / Jivan, A. / Dollins, D.E. / Claessens, F. / Gewirth, D.T.
History
DepositionOct 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: 5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*CP*AP*AP*GP*AP*AP*CP*AP*G)-3'
D: 5'-D(*CP*TP*GP*TP*TP*CP*TP*TP*GP*AP*TP*GP*TP*TP*CP*TP*GP*G)-3'
A: Androgen receptor
B: Androgen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5908
Polymers34,3284
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.89, 137.89, 85.71
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: DNA chain 5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*CP*AP*AP*GP*AP*AP*CP*AP*G)-3'


Mass: 5511.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Androgen Direct Repeat Response Element
#2: DNA chain 5'-D(*CP*TP*GP*TP*TP*CP*TP*TP*GP*AP*TP*GP*TP*TP*CP*TP*GP*G)-3'


Mass: 5519.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Androgen Direct Repeat Response Element
#3: Protein Androgen receptor / Dihydrotestosterone receptor


Mass: 11648.361 Da / Num. of mol.: 2 / Fragment: DNA-Binding Domain / Mutation: C552A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: AR / Plasmid: pGEX-NB-AR1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15207
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 400, magnesium chloride, Tris, DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2magnesium chloride11
3Tris11
4DTT11
5H2O11
6PEG 40012
7magnesium chloride12
8DTT12
9H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0000, 1.2831
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 9, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.28311
ReflectionResolution: 3.1→50 Å / Num. obs: 17313 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 20.4
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1683 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ER Complex from PDB entry 1HCQ

1hcq


Resolution: 3.1→50 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 258680.39 / Data cutoff high rms absF: 258680.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 725 4.9 %RANDOM
Rwork0.246 ---
obs-14839 85.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.5832 Å2 / ksol: 0.228276 e/Å3
Displacement parametersBiso mean: 117.7 Å2
Baniso -1Baniso -2Baniso -3
1-41.29 Å229.66 Å20 Å2
2--41.29 Å20 Å2
3----82.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.64 Å
Luzzati d res low-5 Å
Luzzati sigma a1.2 Å1.08 Å
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1077 732 4 0 1813
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.72
X-RAY DIFFRACTIONc_scbond_it1.242
X-RAY DIFFRACTIONc_scangle_it2.12.5
LS refinement shellResolution: 3.1→3.21 Å / Rfactor Rfree error: 0.094 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.6 41 3.9 %
Rwork0.564 998 -
obs--60.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4PARAM_ZN

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