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- PDB-3btr: AR-NLS:Importin-alpha complex -

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Basic information

Entry
Database: PDB / ID: 3btr
TitleAR-NLS:Importin-alpha complex
Components
  • Androgen receptor
  • Importin subunit alpha-2
KeywordsHORMONE / importin-alpha-androgen receptor complex / Cytoplasm / Nucleus / Phosphoprotein / Protein transport / Transport / Disease mutation / DNA-binding / Lipid-binding / Metal-binding / Polymorphism / Steroid-binding / Transcription / Transcription regulation / Triplet repeat expansion / Ubl conjugation / Zinc / Zinc-finger
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 / Sensing of DNA Double Strand Breaks ...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 / Sensing of DNA Double Strand Breaks / animal organ formation / androgen binding / entry of viral genome into host nucleus through nuclear pore complex via importin / Leydig cell differentiation / regulation of systemic arterial blood pressure / epithelial cell morphogenesis / prostate gland growth / positive regulation of viral life cycle / 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 / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / host cell / positive regulation of transcription by RNA polymerase III / RNA polymerase II general transcription initiation factor binding / positive regulation of insulin-like growth factor receptor signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / positive regulation of intracellular estrogen receptor signaling pathway / NLS-bearing protein import into nucleus / morphogenesis of an epithelial fold / cellular response to steroid hormone stimulus / seminiferous tubule development / single fertilization / androgen receptor signaling pathway / RUNX2 regulates osteoblast differentiation / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / regulation of protein localization to plasma membrane / intracellular steroid hormone receptor signaling pathway / positive regulation of phosphorylation / 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 / G protein-coupled receptor activity / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of cell differentiation / multicellular organism growth / SUMOylation of intracellular receptors / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / transcription coactivator binding / beta-catenin binding / positive regulation of miRNA transcription / cytoplasmic stress granule / Nuclear Receptor transcription pathway / protein import into nucleus / histone deacetylase binding / male gonad development / nuclear receptor activity / negative regulation of epithelial cell proliferation / 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 / nuclear membrane / DNA-binding transcription factor binding / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / postsynaptic density / positive regulation of MAPK cascade / transcription by RNA polymerase II / molecular adaptor activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / signaling receptor binding / glutamatergic synapse / chromatin binding / positive regulation of cell population proliferation / chromatin / positive regulation of gene expression / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding
Similarity search - Function
Androgen receptor / Androgen receptor / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. ...Androgen receptor / Androgen receptor / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / 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 / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Androgen receptor / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCutress, M.L. / Whitaker, H.C. / Mills, I.G. / Stewart, M. / Neal, D.E.
CitationJournal: J.Cell.Sci. / Year: 2008
Title: Structural basis for the nuclear import of the human androgen receptor
Authors: Cutress, M.L. / Whitaker, H.C. / Mills, I.G. / Stewart, M. / Neal, D.E.
History
DepositionDec 30, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Importin subunit alpha-2
B: Androgen receptor


Theoretical massNumber of molelcules
Total (without water)47,8762
Polymers47,8762
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-3.6 kcal/mol
Surface area18830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.274, 89.372, 98.104
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 Importin subunit alpha-2 / / Karyopherin subunit alpha-2 / SRP1-alpha / RAG cohort protein 1 / Pendulin / Pore targeting complex ...Karyopherin subunit alpha-2 / SRP1-alpha / RAG cohort protein 1 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / Importin alpha P1


Mass: 46298.977 Da / Num. of mol.: 1 / Fragment: UNP residues 70-496
Source method: isolated from a genetically manipulated source
Details: See publication for complete details of expression, purification, and characterization
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P52293
#2: Protein/peptide Androgen receptor / / Dihydrotestosterone receptor / Nuclear receptor subfamily 3 group C member 4


Mass: 1576.946 Da / Num. of mol.: 1 / Fragment: UNP residues 621-635
Source method: isolated from a genetically manipulated source
Details: See publication for complete details of expression, characterization and purification
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P10275
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.58 Å3/Da / Density % sol: 65.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 28, 2005 / Details: mirrors
RadiationMonochromator: Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.576→21.393 Å / Num. all: 2765 / Num. obs: 21477 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 8
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.262 / % possible all: 88.1

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
MAR345dtbdata collection
REFMAC5.2.001phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EJY

1ejy


Resolution: 2.6→20.11 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 8.422 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 1454 6.8 %RANDOM
Rwork0.18568 ---
obs0.18859 19981 98.61 %-
all-2765 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.892 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å20 Å20 Å2
2---2.02 Å20 Å2
3---4.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.6→20.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3363 0 0 33 3396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223420
X-RAY DIFFRACTIONr_bond_other_d0.0010.022250
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.9714653
X-RAY DIFFRACTIONr_angle_other_deg0.9135576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.375440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.86425.896134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.27115600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3841512
X-RAY DIFFRACTIONr_chiral_restr0.0670.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023761
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02592
X-RAY DIFFRACTIONr_nbd_refined0.2340.2913
X-RAY DIFFRACTIONr_nbd_other0.1810.22387
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21743
X-RAY DIFFRACTIONr_nbtor_other0.0880.21754
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.277
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1220.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1510.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.66352838
X-RAY DIFFRACTIONr_mcbond_other0.5965891
X-RAY DIFFRACTIONr_mcangle_it4.906103555
X-RAY DIFFRACTIONr_scbond_it3.34551383
X-RAY DIFFRACTIONr_scangle_it4.88101098
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 74 -
Rwork0.245 1191 -
obs--81.09 %

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