[English] 日本語
Yorodumi
- PDB-2nw4: Crystal Structure of the Rat Androgen Receptor Ligand Binding Dom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2nw4
TitleCrystal Structure of the Rat Androgen Receptor Ligand Binding Domain Complex with BMS-564929
ComponentsAndrogen receptor
KeywordsHORMONE/GROWTH FACTOR / ANDROGEN RECEPTOR / STEROID RECEPTOR / NUCLEAR RECEPTOR / TRANSCRIPTION REGULATION / LIGAND-BINDING DOMAIN / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


reproductive behavior / male somatic sex determination / prostate induction / lateral sprouting involved in mammary gland duct morphogenesis / tertiary branching involved in mammary gland duct morphogenesis / morphogenesis of an epithelial fold / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / male sex differentiation / copulation / regulation of developmental growth ...reproductive behavior / male somatic sex determination / prostate induction / lateral sprouting involved in mammary gland duct morphogenesis / tertiary branching involved in mammary gland duct morphogenesis / morphogenesis of an epithelial fold / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / male sex differentiation / copulation / regulation of developmental growth / animal organ formation / regulation of prostatic bud formation / male genitalia morphogenesis / seminiferous tubule development / positive regulation of epithelial cell proliferation involved in prostate gland development / skeletal muscle hypertrophy / prostate gland growth / epithelial cell morphogenesis / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / prostate gland epithelium morphogenesis / positive regulation of penile erection / ribonucleotide binding / epithelial cell differentiation involved in prostate gland development / male courtship behavior / Leydig cell differentiation / positive regulation of hippocampal neuron apoptotic process / regulation of systemic arterial blood pressure / response to environmental enrichment / reproductive system development / Ub-specific processing proteases / mammary gland alveolus development / reproductive structure development / POU domain binding / drinking behavior / positive regulation of integrin biosynthetic process / fertilization / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / cellular response to testosterone stimulus / positive regulation of locomotion / androgen binding / cellular response to follicle-stimulating hormone stimulus / positive regulation of insulin-like growth factor receptor signaling pathway / androgen receptor signaling pathway / positive regulation of intracellular estrogen receptor signaling pathway / membraneless organelle assembly / locomotion / RNA polymerase II general transcription initiation factor binding / response to steroid hormone / single fertilization / response to muscle activity / multicellular organism growth / nuclear androgen receptor binding / cellular response to steroid hormone stimulus / response to testosterone / nuclear steroid receptor activity / positive regulation of transcription by RNA polymerase III / cellular response to estrogen stimulus / estrogen response element binding / estrogen receptor signaling pathway / RNA polymerase II core promoter sequence-specific DNA binding / regulation of protein localization to plasma membrane / intracellular receptor signaling pathway / steroid binding / male gonad development / in utero embryonic development / liver regeneration / gene expression / negative regulation of extrinsic apoptotic signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / response to nicotine / positive regulation of cell differentiation / molecular condensate scaffold activity / response to insulin / negative regulation of epithelial cell proliferation / positive regulation of miRNA transcription / beta-catenin binding / nuclear receptor activity / transcription coactivator binding / nuclear matrix / regulation of gene expression / response to estradiol / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / sequence-specific DNA binding / molecular adaptor activity / response to ethanol / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of MAPK cascade / nuclear speck / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / signaling receptor binding / protein domain specific binding / axon / negative regulation of DNA-templated transcription / positive regulation of gene expression
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 / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors ...Androgen receptor / Androgen receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / 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-8NH / Androgen receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 3 Å
AuthorsOstrowski, J. / Kuhns, J.E. / Lupisella, J.A. / Manfredi, M.C. / Beehler, B.C. / Krystek, S.R. / Bi, Y. / Sun, C. / Seethala, R. / Golla, R. ...Ostrowski, J. / Kuhns, J.E. / Lupisella, J.A. / Manfredi, M.C. / Beehler, B.C. / Krystek, S.R. / Bi, Y. / Sun, C. / Seethala, R. / Golla, R. / Sleph, P.G. / Fura, A. / An, Y. / Kish, K.F. / Sack, J.S. / Mookhtiar, K.A. / Grover, G.J. / Hamann, L.G.
CitationJournal: Endocrinology / Year: 2007
Title: Pharmacological and x-ray structural characterization of a novel selective androgen receptor modulator: potent hyperanabolic stimulation of skeletal muscle with hypostimulation of prostate in rats.
Authors: Ostrowski, J. / Kuhns, J.E. / Lupisella, J.A. / Manfredi, M.C. / Beehler, B.C. / Krystek, S.R. / Bi, Y. / Sun, C. / Seethala, R. / Golla, R. / Sleph, P.G. / Fura, A. / An, Y. / Kish, K.F. / ...Authors: Ostrowski, J. / Kuhns, J.E. / Lupisella, J.A. / Manfredi, M.C. / Beehler, B.C. / Krystek, S.R. / Bi, Y. / Sun, C. / Seethala, R. / Golla, R. / Sleph, P.G. / Fura, A. / An, Y. / Kish, K.F. / Sack, J.S. / Mookhtiar, K.A. / Grover, G.J. / Hamann, L.G.
History
DepositionNov 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Androgen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5882
Polymers30,2821
Non-polymers3061
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.640, 65.620, 70.830
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


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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P15207
#2: Chemical ChemComp-8NH / 2-CHLORO-4-[(7R,7AS)-7-HYDROXY-1,3-DIOXOTETRAHYDRO-1H-PYRROLO[1,2-C]IMIDAZOL-2(3H)-YL]-3-METHYLBENZONITRILE


Mass: 305.716 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12ClN3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.34 Å3/Da / Density % sol: 42.36 %
Crystal growMethod: vapor diffusion, hanging drop
Details: 0.88M NA TARTRATE, 0.1M NA HEPES, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 24, 2002 / Details: "BLUE" CONFOCAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. obs: 5527 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 13
Reflection shellResolution: 3→3.11 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 3.4 / % possible all: 98.5

-
Processing

Software
NameClassification
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
RefinementMethod to determine structure: molecular replacement
Starting model: 1I37

1i37


Resolution: 3→18.2 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 895069.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.293 304 5.5 %RANDOM
Rwork0.249 ---
obs-5481 99.8 %-
Displacement parametersBiso mean: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1-21.8 Å20 Å20 Å2
2---10.31 Å20 Å2
3----11.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 3→18.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 21 8 2031
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.009
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.4
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d20.5
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d1.05
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it1.291.5
X-RAY DIFFRACTIONo_mcangle_it2.272
X-RAY DIFFRACTIONo_scbond_it1.812
X-RAY DIFFRACTIONo_scangle_it2.862.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 51 5.8 %
Rwork0.272 832 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4bms-564929.parbms-564929.top

+
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