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- PDB-2q7j: The Wild Type Androgen Receptor Ligand Binding Domain Bound with ... -

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Basic information

Entry
Database: PDB / ID: 2q7j
TitleThe Wild Type Androgen Receptor Ligand Binding Domain Bound with Testosterone and a TIF2 box 3 Coactivator Peptide 740-753
Components
  • Androgen receptor
  • Nuclear receptor coactivator 2
KeywordsHORMONE / androgen receptor steroid nuclear receptor ligand binding domain / testoseterone / TIF2 boxIII coactivator peptide
Function / homology
Function and homology information


male somatic sex determination / activation of prostate induction by androgen receptor signaling pathway / 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 / tertiary branching involved in mammary gland duct morphogenesis / animal organ formation ...male somatic sex determination / activation of prostate induction by androgen receptor signaling pathway / 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 / 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 / non-membrane-bounded organelle assembly / positive regulation of epithelial cell proliferation involved in prostate gland development / prostate gland epithelium morphogenesis / intracellular receptor signaling pathway / cellular response to testosterone stimulus / 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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / cellular response to steroid hormone stimulus / morphogenesis of an epithelial fold / seminiferous tubule development / androgen receptor signaling pathway / RUNX2 regulates osteoblast differentiation / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / single fertilization / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / regulation of protein localization to plasma membrane / Endogenous sterols / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / intracellular steroid hormone receptor signaling pathway / positive regulation of phosphorylation / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / positive regulation of adipose tissue development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / steroid binding / insulin-like growth factor receptor signaling pathway / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / epithelial cell proliferation / molecular condensate scaffold activity / response to progesterone / G protein-coupled receptor activity / nuclear receptor binding / positive regulation of cell differentiation / negative regulation of extrinsic apoptotic signaling pathway / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / multicellular organism growth / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / transcription coactivator binding / positive regulation of miRNA transcription / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / negative regulation of epithelial cell proliferation / male gonad development / MAPK cascade / Circadian Clock / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / HATs acetylate histones / ATPase binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II
Similarity search - Function
Androgen receptor / Androgen receptor / Nuclear receptor coactivator 2 / 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 ...Androgen receptor / Androgen receptor / Nuclear receptor coactivator 2 / 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 DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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
TESTOSTERONE / Androgen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGampe, R.T.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Modulation of androgen receptor activation function 2 by testosterone and dihydrotestosterone.
Authors: Askew, E.B. / Gampe, R.T. / Stanley, T.B. / Faggart, J.L. / Wilson, E.M.
History
DepositionJun 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1935
Polymers31,7162
Non-polymers4773
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.779, 66.871, 70.237
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: 30007.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AR, DHTR, NR3C4 / Production host: Escherichia coli (E. coli) / References: UniProt: P10275
#2: Protein/peptide Nuclear receptor coactivator 2 / / NCoA-2 / Transcriptional intermediary factor 2


Mass: 1708.931 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOA2, TIF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15596

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Non-polymers , 4 types, 161 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TES / TESTOSTERONE / Testosterone


Mass: 288.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28O2 / Comment: hormone*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.03 Å3/Da / Density % sol: 39.33 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→20.55 Å / Num. obs: 20209 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.44 / Net I/σ(I): 47.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2042 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20.55 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.613 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22027 677 3.2 %RANDOM
Rwork0.18023 ---
obs0.18153 20209 99.89 %-
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: 28.721 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 32 158 2285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222232
X-RAY DIFFRACTIONr_bond_other_d0.0010.022064
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.9713038
X-RAY DIFFRACTIONr_angle_other_deg0.77834793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4115274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.08723.942104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28415390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8611513
X-RAY DIFFRACTIONr_chiral_restr0.0640.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022436
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02463
X-RAY DIFFRACTIONr_nbd_refined0.2120.2531
X-RAY DIFFRACTIONr_nbd_other0.1730.22036
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21107
X-RAY DIFFRACTIONr_nbtor_other0.0830.21104
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2126
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1780.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.210
X-RAY DIFFRACTIONr_mcbond_it0.761.51362
X-RAY DIFFRACTIONr_mcbond_other0.1211.5530
X-RAY DIFFRACTIONr_mcangle_it1.24922153
X-RAY DIFFRACTIONr_scbond_it1.5743977
X-RAY DIFFRACTIONr_scangle_it2.394.5876
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 53 -
Rwork0.248 1435 -
obs--99.13 %

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