[English] 日本語
Yorodumi
- PDB-2qpy: AR LBD with small molecule -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qpy
TitleAR LBD with small molecule
Components
  • Androgen receptor
  • Coactivator peptide
KeywordsDNA BINDING PROTEIN / androgen receptor DHT coactivator / DNA-binding / Lipid-binding / Metal-binding / Nucleus / Steroid-binding / Transcription / Transcription regulation / Ubl conjugation / Zinc / Zinc-finger
Function / homology
Function and homology information


RUNX2 regulates osteoblast differentiation / cellular process / transcription coactivator binding => GO:0001223 / reproductive behavior / DNA-binding transcription factor binding => GO:0140297 / copulation / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / male sex differentiation / SUMOylation of intracellular receptors ...RUNX2 regulates osteoblast differentiation / cellular process / transcription coactivator binding => GO:0001223 / reproductive behavior / DNA-binding transcription factor binding => GO:0140297 / copulation / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / male sex differentiation / SUMOylation of intracellular receptors / skeletal muscle hypertrophy / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / Nuclear Receptor transcription pathway / regulation of prostatic bud formation / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of penile erection / positive regulation of glucocorticoid receptor signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ribonucleotide binding / reproductive system development / Endogenous sterols / male courtship behavior / HATs acetylate histones / 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 / reproductive structure development / male genitalia morphogenesis / positive regulation of integrin biosynthetic process / tertiary branching involved in mammary gland duct morphogenesis / Regulation of lipid metabolism by PPARalpha / chromatin => GO:0000785 / animal organ formation / Cytoprotection by HMOX1 / androgen binding / Leydig cell differentiation / regulation of systemic arterial blood pressure / epithelial cell morphogenesis / Estrogen-dependent gene expression / nuclear glucocorticoid receptor binding / 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 / Ub-specific processing proteases / cellular response to testosterone stimulus / nuclear retinoic acid receptor binding / fertilization / positive regulation of female receptivity / 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 / nuclear thyroid hormone receptor binding / nuclear androgen receptor binding / cellular response to steroid hormone stimulus / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / morphogenesis of an epithelial fold / seminiferous tubule development / androgen receptor signaling pathway / locomotor rhythm / aryl hydrocarbon receptor binding / transcription factor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / single fertilization / mammary gland alveolus development / regulation of protein localization to plasma membrane / estrogen receptor signaling pathway / cellular response to estrogen stimulus / DNA polymerase binding / nuclear retinoid X receptor binding / positive regulation of phosphorylation / regulation of cellular response to insulin stimulus / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / steroid binding / nuclear receptor coactivator activity / response to progesterone / nuclear estrogen receptor binding / nuclear receptor binding / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of cell differentiation / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / multicellular organism growth / beta-catenin binding / circadian rhythm / RNA polymerase II transcription regulator complex / nuclear receptor activity / negative regulation of epithelial cell proliferation / male gonad development
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
Chem-4HY / 5-ALPHA-DIHYDROTESTOSTERONE / Androgen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsEstebanez-Perpina, E. / Fletterick, R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: A surface on the androgen receptor that allosterically regulates coactivator binding.
Authors: Estebanez-Perpina, E. / Arnold, L.A. / Arnold, A.A. / Nguyen, P. / Rodrigues, E.D. / Mar, E. / Bateman, R. / Pallai, P. / Shokat, K.M. / Baxter, J.D. / Guy, R.K. / Webb, P. / Fletterick, R.J.
History
DepositionJul 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Source and taxonomy / Structure summary
Category: entity / pdbx_entity_src_syn / software
Item: _entity.pdbx_description / _software.classification / _software.name
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Androgen receptor
B: Coactivator peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4554
Polymers30,5432
Non-polymers9122
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.790, 66.680, 72.080
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: 29277.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ar, Nr3c4 / Production host: Escherichia coli (E. coli) / References: UniProt: P19091
#2: Protein/peptide Coactivator peptide


Mass: 1265.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q61026*PLUS
#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: Chemical ChemComp-4HY / [4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID


Mass: 621.932 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H9I3O4 / Comment: hormone*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growMethod: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. all: 11046 / Num. obs: 9407 / Rmerge(I) obs: 0.093
Reflection shellHighest resolution: 2.5 Å

-
Processing

Software
NameClassification
ELVESrefinement
CNSrefinement
ELVESdata reduction
ELVESdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→100 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.269 -
Rwork0.269 -
obs0.269 9407
all-11046
Refinement stepCycle: LAST / Resolution: 2.5→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2117 0 42 24 2183

+
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://pdbjlvh1.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