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- PDB-3l3z: Crystal structure of DHT-bound androgen receptor in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3l3z
TitleCrystal structure of DHT-bound androgen receptor in complex with the third motif of steroid receptor coactivator 3
Components
  • Androgen receptor
  • Nuclear receptor coactivator 3
KeywordsPROTEIN BINDING / androgen receptor / ligand binding domain / steroid receptor coactivator 3 / 5-alpha-dihydrotestosterone (DHT) / prostate cancer
Function / homology
Function and homology information


receptor transactivation / cell dedifferentiation / regulation of stem cell division / male somatic sex determination / : / lateral sprouting involved in mammary gland duct morphogenesis / POU domain binding / negative regulation of integrin biosynthetic process / regulation of developmental growth / male genitalia morphogenesis ...receptor transactivation / cell dedifferentiation / regulation of stem cell division / male somatic sex determination / : / lateral sprouting involved in mammary gland duct morphogenesis / POU domain binding / negative regulation of integrin biosynthetic process / regulation of developmental growth / male genitalia morphogenesis / positive regulation of integrin biosynthetic process / intracellular receptor signaling pathway / tertiary branching involved in mammary gland duct morphogenesis / animal organ formation / 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 / membraneless organelle assembly / prostate gland epithelium morphogenesis / cellular response to testosterone stimulus / positive regulation of keratinocyte differentiation / vitamin D receptor signaling pathway / RNA polymerase II general transcription initiation factor binding / positive regulation of insulin-like growth factor receptor signaling pathway / nuclear thyroid hormone receptor binding / positive regulation of intracellular estrogen receptor signaling pathway / positive regulation of transcription by RNA polymerase III / cellular response to steroid hormone stimulus / morphogenesis of an epithelial fold / positive regulation of stem cell population maintenance / seminiferous tubule development / androgen receptor signaling pathway / RNA polymerase II complex binding / RUNX2 regulates osteoblast differentiation / single fertilization / mammary gland alveolus development / regulation of protein localization to plasma membrane / cellular response to estrogen stimulus / estrogen response element binding / retinoic acid receptor signaling pathway / nuclear receptor-mediated steroid hormone signaling pathway / histone acetyltransferase activity / positive regulation of phosphorylation / histone acetyltransferase / cellular response to hormone stimulus / estrogen receptor signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / steroid binding / insulin-like growth factor receptor signaling pathway / epithelial cell proliferation / nuclear receptor coactivator activity / cellular response to estradiol stimulus / nuclear receptor binding / negative regulation of extrinsic apoptotic signaling pathway / G protein-coupled receptor activity / positive regulation of cell differentiation / molecular condensate scaffold activity / SUMOylation of intracellular receptors / MAPK6/MAPK4 signaling / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PPARA activates gene expression / multicellular organism growth / beta-catenin binding / transcription coactivator binding / positive regulation of miRNA transcription / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / male gonad development / nuclear receptor activity / negative regulation of epithelial cell proliferation / disordered domain specific binding / MAPK cascade / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / ATPase binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription by RNA polymerase II / positive regulation of MAPK cascade / molecular adaptor activity / transcription coactivator activity / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / nuclear speck / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / signaling receptor binding / chromatin binding / positive regulation of cell population proliferation
Similarity search - Function
Androgen receptor / Androgen receptor / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 ...Androgen receptor / Androgen receptor / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / : / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / 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 / Nuclear receptor coactivator 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhou, X.E. / Suino-Powell, K.M. / Li, J. / He, A. / MacKeigan, J.P. / Melcher, K. / Yong, E.-L. / Xu, H.E.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Identification of SRC3/AIB1 as a Preferred Coactivator for Hormone-activated Androgen Receptor.
Authors: Zhou, X.E. / Suino-Powell, K.M. / Li, J. / He, Y. / Mackeigan, J.P. / Melcher, K. / Yong, E.L. / Xu, H.E.
History
DepositionDec 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Androgen receptor
B: Nuclear receptor coactivator 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9023
Polymers30,6122
Non-polymers2901
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-10 kcal/mol
Surface area12450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.427, 66.830, 72.494
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 / Nuclear receptor subfamily 3 group C member 4


Mass: 29133.148 Da / Num. of mol.: 1 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AR, DHTR, NR3C4 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10275
#2: Protein/peptide Nuclear receptor coactivator 3


Mass: 1478.652 Da / Num. of mol.: 1 / Fragment: receptor binding motif 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y6Q9
#3: Chemical ChemComp-DHT / 5-ALPHA-DIHYDROTESTOSTERONE


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


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, pH 7.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 24, 2006
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 18358 / Num. obs: 17278 / % possible obs: 85.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 17
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.005data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.566 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24263 1320 7.2 %RANDOM
Rwork0.1928 ---
obs0.19616 16921 95.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.32 Å2
Baniso -1Baniso -2Baniso -3
1-2.39 Å20 Å20 Å2
2---1.66 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2135 0 21 141 2297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222210
X-RAY DIFFRACTIONr_bond_other_d0.0010.021540
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.972990
X-RAY DIFFRACTIONr_angle_other_deg0.91133744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8495258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87123.558104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52215397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.111515
X-RAY DIFFRACTIONr_chiral_restr0.0880.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212376
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02459
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.611.51305
X-RAY DIFFRACTIONr_mcbond_other0.5591.5517
X-RAY DIFFRACTIONr_mcangle_it2.77222114
X-RAY DIFFRACTIONr_scbond_it3.4333905
X-RAY DIFFRACTIONr_scangle_it5.0284.5876
X-RAY DIFFRACTIONr_rigid_bond_restr2.19333750
X-RAY DIFFRACTIONr_sphericity_free12.2355141
X-RAY DIFFRACTIONr_sphericity_bonded3.77353696
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 82 -
Rwork0.251 910 -
obs--72.46 %

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