[English] 日本語
Yorodumi
- PDB-1r4i: Crystal Structure of Androgen Receptor DNA-Binding Domain Bound t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1r4i
TitleCrystal Structure of Androgen Receptor DNA-Binding Domain Bound to a Direct Repeat Response Element
Components
  • 5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*CP*AP*AP*GP*AP*AP*CP*AP*G)-3'
  • 5'-D(*CP*TP*GP*TP*TP*CP*TP*TP*GP*AP*TP*GP*TP*TP*CP*TP*GP*G)-3'
  • Androgen receptor
KeywordsTRANSCRIPTION/DNA / AR / Steroid Receptor / Protein-DNA Complex / Androgen / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


negative regulation of integrin biosynthetic process / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / copulation / male sex differentiation / skeletal muscle hypertrophy / positive regulation of penile erection / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of locomotion / regulation of prostatic bud formation / ribonucleotide binding ...negative regulation of integrin biosynthetic process / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / copulation / male sex differentiation / skeletal muscle hypertrophy / positive regulation of penile erection / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of locomotion / regulation of prostatic bud formation / ribonucleotide binding / male courtship behavior / positive regulation of hippocampal neuron apoptotic process / male somatic sex determination / prostate induction / lateral sprouting involved in mammary gland duct morphogenesis / Ub-specific processing proteases / male genitalia morphogenesis / POU domain binding / regulation of developmental growth / positive regulation of integrin biosynthetic process / reproductive structure development / SUMOylation of intracellular receptors / tertiary branching involved in mammary gland duct morphogenesis / Nuclear Receptor transcription pathway / animal organ formation / androgen binding / drinking behavior / response to environmental enrichment / cellular response to testosterone stimulus / cellular response to follicle-stimulating hormone stimulus / regulation of systemic arterial blood pressure / reproductive behavior / Leydig cell differentiation / epithelial cell differentiation involved in prostate gland development / seminiferous tubule development / positive regulation of epithelial cell proliferation involved in prostate gland development / prostate gland epithelium morphogenesis / prostate gland growth / epithelial cell morphogenesis / membraneless organelle assembly / reproductive system development / locomotion / fertilization / RNA polymerase II general transcription initiation factor binding / positive regulation of insulin-like growth factor receptor signaling pathway / response to steroid hormone / positive regulation of transcription by RNA polymerase III / nuclear androgen receptor binding / cellular response to steroid hormone stimulus / morphogenesis of an epithelial fold / positive regulation of intracellular estrogen receptor signaling pathway / androgen receptor signaling pathway / response to testosterone / response to muscle activity / positive regulation of phosphorylation / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / single fertilization / regulation of protein localization to plasma membrane / RNA polymerase II core promoter sequence-specific DNA binding / intracellular receptor signaling pathway / estrogen receptor signaling pathway / steroid binding / liver regeneration / insulin-like growth factor receptor signaling pathway / epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / response to nicotine / positive regulation of cell differentiation / molecular condensate scaffold activity / response to insulin / beta-catenin binding / positive regulation of miRNA transcription / transcription coactivator binding / nuclear matrix / multicellular organism growth / male gonad development / nuclear receptor activity / negative regulation of epithelial cell proliferation / response to estradiol / MAPK cascade / regulation of gene expression / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / spermatogenesis / molecular adaptor activity / gene expression / sequence-specific DNA binding / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription cis-regulatory region binding / positive regulation of MAPK cascade / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / axon
Similarity search - Function
Androgen receptor / Androgen receptor / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / : / 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 / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / : / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Androgen receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsShaffer, P.L. / Jivan, A. / Dollins, D.E. / Claessens, F. / Gewirth, D.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structural basis of androgen receptor binding to selective androgen response elements.
Authors: Shaffer, P.L. / Jivan, A. / Dollins, D.E. / Claessens, F. / Gewirth, D.T.
History
DepositionOct 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: 5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*CP*AP*AP*GP*AP*AP*CP*AP*G)-3'
D: 5'-D(*CP*TP*GP*TP*TP*CP*TP*TP*GP*AP*TP*GP*TP*TP*CP*TP*GP*G)-3'
A: Androgen receptor
B: Androgen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5908
Polymers34,3284
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.89, 137.89, 85.71
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: DNA chain 5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*CP*AP*AP*GP*AP*AP*CP*AP*G)-3'


Mass: 5511.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Androgen Direct Repeat Response Element
#2: DNA chain 5'-D(*CP*TP*GP*TP*TP*CP*TP*TP*GP*AP*TP*GP*TP*TP*CP*TP*GP*G)-3'


Mass: 5519.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Androgen Direct Repeat Response Element
#3: Protein Androgen receptor / Dihydrotestosterone receptor


Mass: 11648.361 Da / Num. of mol.: 2 / Fragment: DNA-Binding Domain / Mutation: C552A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: AR / Plasmid: pGEX-NB-AR1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15207
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 400, magnesium chloride, Tris, DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2magnesium chloride11
3Tris11
4DTT11
5H2O11
6PEG 40012
7magnesium chloride12
8DTT12
9H2O12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0000, 1.2831
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 9, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.28311
ReflectionResolution: 3.1→50 Å / Num. obs: 17313 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 20.4
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1683 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ER Complex from PDB entry 1HCQ

1hcq


Resolution: 3.1→50 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 258680.39 / Data cutoff high rms absF: 258680.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 725 4.9 %RANDOM
Rwork0.246 ---
obs-14839 85.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.5832 Å2 / ksol: 0.228276 e/Å3
Displacement parametersBiso mean: 117.7 Å2
Baniso -1Baniso -2Baniso -3
1-41.29 Å229.66 Å20 Å2
2--41.29 Å20 Å2
3----82.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.64 Å
Luzzati d res low-5 Å
Luzzati sigma a1.2 Å1.08 Å
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1077 732 4 0 1813
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.72
X-RAY DIFFRACTIONc_scbond_it1.242
X-RAY DIFFRACTIONc_scangle_it2.12.5
LS refinement shellResolution: 3.1→3.21 Å / Rfactor Rfree error: 0.094 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.6 41 3.9 %
Rwork0.564 998 -
obs--60.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4PARAM_ZN

+
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