[English] 日本語
Yorodumi
- PDB-3g0w: Crystal structure of the rat androgen receptor ligand binding dom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3g0w
TitleCrystal structure of the rat androgen receptor ligand binding domain complex with an n-aryl-oxazolidin 2-imine inhibitor
ComponentsAndrogen receptor
KeywordsHORMONE / ANDROGEN RECEPTOR / STEROID RECEPTOR / NUCLEAR RECEPTOR / TRANSCRIPTION REGULATION / LIGAND-BINDING DOMAIN / Disease mutation / DNA-binding / Lipid-binding / Metal-binding / Nucleus / Phosphoprotein / Receptor / Steroid-binding / Transcription / Ubl conjugation / Zinc / Zinc-finger / HORMONE-GROWTH FACTOR 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 / male courtship behavior / ribonucleotide binding ...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 / male courtship behavior / ribonucleotide binding / reproductive system development / 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 / 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 / positive regulation of intracellular estrogen receptor signaling pathway / nuclear androgen receptor binding / morphogenesis of an epithelial fold / cellular response to steroid hormone stimulus / response to testosterone / seminiferous tubule development / single fertilization / androgen receptor signaling pathway / 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 / steroid binding / insulin-like growth factor receptor signaling pathway / epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of cell differentiation / multicellular organism growth / response to insulin / transcription coactivator binding / beta-catenin binding / positive regulation of miRNA transcription / male gonad development / nuclear receptor activity / negative regulation of epithelial cell proliferation / 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 / positive regulation of MAPK cascade / transcription by RNA polymerase II / 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 / axon / protein domain specific binding / negative regulation of cell population proliferation / signaling receptor binding / negative regulation of DNA-templated transcription / dendrite / chromatin binding / positive regulation of cell population proliferation / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding
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 / Nuclear hormone receptor, ligand-binding domain ...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
Chem-LGB / Androgen receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.95 Å
AuthorsSack, J.S.
CitationJournal: J.Med.Chem. / Year: 2009
Title: N-aryl-oxazolidin-2-imine muscle selective androgen receptor modulators enhance potency through pharmacophore reorientation.
Authors: Nirschl, A.A. / Zou, Y. / Krystek, S.R. / Sutton, J.C. / Simpkins, L.M. / Lupisella, J.A. / Kuhns, J.E. / Seethala, R. / Golla, R. / Sleph, P.G. / Beehler, B.C. / Grover, G.J. / Egan, D. / ...Authors: Nirschl, A.A. / Zou, Y. / Krystek, S.R. / Sutton, J.C. / Simpkins, L.M. / Lupisella, J.A. / Kuhns, J.E. / Seethala, R. / Golla, R. / Sleph, P.G. / Beehler, B.C. / Grover, G.J. / Egan, D. / Fura, A. / Vyas, V.P. / Li, Y.X. / Sack, J.S. / Kish, K.F. / An, Y. / Bryson, J.A. / Gougoutas, J.Z. / DiMarco, J. / Zahler, R. / Ostrowski, J. / Hamann, L.G.
History
DepositionJan 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Androgen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6422
Polymers30,2821
Non-polymers3601
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.862, 65.739, 69.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Androgen receptor / / Dihydrotestosterone receptor / Nuclear receptor subfamily 3 group C member 4


Mass: 30282.414 Da / Num. of mol.: 1 / Fragment: Ligand-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ar, Nr3c4 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P15207
#2: Chemical ChemComp-LGB / 2-chloro-4-{[(1R,3Z,7S,7aS)-7-hydroxy-1-(trifluoromethyl)tetrahydro-1H-pyrrolo[1,2-c][1,3]oxazol-3-ylidene]amino}-3-met hylbenzonitrile / 3,11-DIFLUORO-6,8,13-TRIMETHYL-8H-QUINO[4,3,2-KL]ACRIDIN-13-IUM


Mass: 359.731 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13ClF3N3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growDetails: 0.88M NA TARTRATE, 0.1M NA HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1
DetectorType: MAR / Detector: CCD / Date: Dec 11, 2003 / Details: MICROMAX CONFOCAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 18851 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 30.596 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 20.6
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 4.6 / % possible all: 100

-
Processing

Software
NameVersionClassification
AMoREphasing
BUSTER-TNT2.5.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: molecular replacement / Resolution: 1.95→47.84 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 669 3.58 %RANDOM
Rwork0.2 ---
obs0.2014 18689 98.34 %-
Displacement parametersBiso mean: 34.51 Å2
Baniso -1Baniso -2Baniso -3
1--7.63131135 Å20 Å20 Å2
2--8.55388617 Å20 Å2
3----0.92257482 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 24 171 2229
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00521112
X-RAY DIFFRACTIONt_angle_deg0.80628452
X-RAY DIFFRACTIONt_dihedral_angle_d20.9714230
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.005482
X-RAY DIFFRACTIONt_gen_planes0.013005
X-RAY DIFFRACTIONt_it1.179211120
X-RAY DIFFRACTIONt_nbd0.032305
LS refinement shellResolution: 1.95→2.07 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3411 109 3.77 %
Rwork0.2937 2779 -
all0.2953 2888 -
obs--98.34 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more