[English] 日本語
Yorodumi
- PDB-7ztx: Crystal structure of mutant AR-LBD (F755V) bound to dihydrotestos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ztx
TitleCrystal structure of mutant AR-LBD (F755V) bound to dihydrotestosterone
ComponentsAndrogen receptor
KeywordsDNA BINDING PROTEIN / Hormone Receptor / Nuclear Receptor / DHT Receptor
Function / homology
Function and homology information


male somatic sex determination / : / 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 / intracellular receptor signaling pathway / tertiary branching involved in mammary gland duct morphogenesis ...male somatic sex determination / : / 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 / intracellular receptor signaling pathway / 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 / positive regulation of epithelial cell proliferation involved in prostate gland development / membraneless organelle assembly / prostate gland epithelium morphogenesis / 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 intracellular estrogen receptor signaling pathway / positive regulation of transcription by RNA polymerase III / cellular response to steroid hormone stimulus / morphogenesis of an epithelial fold / seminiferous tubule development / androgen receptor signaling pathway / RUNX2 regulates osteoblast differentiation / single fertilization / mammary gland alveolus development / regulation of protein localization to plasma membrane / cellular response to estrogen stimulus / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of phosphorylation / estrogen receptor signaling pathway / 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 / negative regulation of extrinsic apoptotic signaling pathway / G protein-coupled receptor activity / positive regulation of cell differentiation / molecular condensate scaffold activity / SUMOylation of intracellular receptors / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / multicellular organism growth / beta-catenin binding / transcription coactivator binding / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / 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 / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / positive regulation of MAPK cascade / molecular adaptor activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / nuclear speck / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / signaling receptor binding / chromatin binding / positive regulation of cell population proliferation / positive regulation of gene expression / chromatin / 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 / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Androgen receptor / Androgen 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 ...Androgen receptor / Androgen 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
Similarity search - Domain/homology
5-ALPHA-DIHYDROTESTOSTERONE / IMIDAZOLE / Androgen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsAlegre-Marti, A. / Jimenez-Panizo, A. / Estebanez-Perpina, E. / Fuentes-Prior, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2023
Title: A hotspot for posttranslational modifications on the androgen receptor dimer interface drives pathology and anti-androgen resistance.
Authors: Alegre-Marti, A. / Jimenez-Panizo, A. / Martinez-Tebar, A. / Poulard, C. / Peralta-Moreno, M.N. / Abella, M. / Anton, R. / Chinas, M. / Eckhard, U. / Piulats, J.M. / Rojas, A.M. / Fernandez- ...Authors: Alegre-Marti, A. / Jimenez-Panizo, A. / Martinez-Tebar, A. / Poulard, C. / Peralta-Moreno, M.N. / Abella, M. / Anton, R. / Chinas, M. / Eckhard, U. / Piulats, J.M. / Rojas, A.M. / Fernandez-Recio, J. / Rubio-Martinez, J. / Le Romancer, M. / Aytes, A. / Fuentes-Prior, P. / Estebanez-Perpina, E.
History
DepositionMay 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Androgen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5505
Polymers28,9981
Non-polymers5524
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, immunoprecipitation, mass spectrometry, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-20 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.573, 65.824, 70.369
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 28998.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Mutation F755V / Source: (gene. exp.) Homo sapiens (human) / Gene: AR, DHTR, NR3C4 / Production host: Escherichia coli (E. coli) / References: UniProt: P10275
#2: Chemical ChemComp-DHT / 5-ALPHA-DIHYDROTESTOSTERONE


Mass: 290.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate HEPES urea

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.89 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.89 Å / Relative weight: 1
ReflectionResolution: 1.89→65.82 Å / Num. obs: 20910 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.045 / Rrim(I) all: 0.116 / Net I/σ(I): 8.8 / Num. measured all: 143549 / Scaling rejects: 19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.89-1.937.23.152945413090.3641.2573.3990.7100
9.06-65.825.40.05512842380.9980.0240.0625.399.6

-
Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T7T

1t7t


Resolution: 1.89→48.07 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.531 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2507 1020 4.9 %RANDOM
Rwork0.2001 ---
obs0.2025 19842 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 128.43 Å2 / Biso mean: 48.192 Å2 / Biso min: 28.88 Å2
Baniso -1Baniso -2Baniso -3
1-4.81 Å20 Å2-0 Å2
2---3.18 Å20 Å2
3----1.64 Å2
Refinement stepCycle: final / Resolution: 1.89→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 36 32 2041
Biso mean--54.54 47.32 -
Num. residues----242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122058
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.622785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1525240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.35821.869107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49215365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2941513
X-RAY DIFFRACTIONr_chiral_restr0.1050.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021509
LS refinement shellResolution: 1.89→1.939 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.519 78 -
Rwork0.417 1454 -
all-1532 -
obs--99.87 %

+
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