[English] 日本語
Yorodumi
- PDB-1t79: Crystal structure of the androgen receptor ligand binding domain ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1t79
TitleCrystal structure of the androgen receptor ligand binding domain in complex with a FxxLW motif
Components
  • Androgen receptor
  • FxxLW motif peptide
KeywordsHORMONE/GROWTH FACTOR RECEPTOR / nuclear receptor / transcription factor / ligand binding domain / AF-2 / androgen / testosterone / DHT / alpha-helical sandwich / HORMONE-GROWTH FACTOR RECEPTOR COMPLEX
Function / homology
Function and homology information


negative regulation of integrin biosynthetic process / androgen binding / intracellular receptor signaling pathway / androgen receptor signaling pathway / estrogen response element binding / regulation of protein localization to plasma membrane / intracellular steroid hormone receptor signaling pathway / positive regulation of phosphorylation / steroid binding / negative regulation of extrinsic apoptotic signaling pathway ...negative regulation of integrin biosynthetic process / androgen binding / intracellular receptor signaling pathway / androgen receptor signaling pathway / estrogen response element binding / regulation of protein localization to plasma membrane / intracellular steroid hormone receptor signaling pathway / positive regulation of phosphorylation / steroid binding / negative regulation of extrinsic apoptotic signaling pathway / beta-catenin binding / male gonad development / nuclear receptor activity / positive regulation of NF-kappaB transcription factor activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / positive regulation of cell population proliferation / chromatin / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm
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
5-ALPHA-DIHYDROTESTOSTERONE / Androgen receptor
Similarity search - Component
Biological speciesPan troglodytes (chimpanzee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHur, E. / Pfaff, S.J. / Payne, E.S. / Gron, H. / Buehrer, B.M. / Fletterick, R.J.
CitationJournal: Plos Biol. / Year: 2004
Title: Recognition and accommodation at the androgen receptor coactivator binding interface.
Authors: Hur, E. / Pfaff, S.J. / Payne, E.S. / Gron, H. / Buehrer, B.M. / Fletterick, R.J.
History
DepositionMay 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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
B: FxxLW motif peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2923
Polymers33,0012
Non-polymers2901
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-10 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.826, 66.128, 68.381
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: 30877.957 Da / Num. of mol.: 1 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pan troglodytes (chimpanzee) / Gene: AR, NR3C4 / Production host: Escherichia coli (E. coli) / References: UniProt: O97775
#2: Protein/peptide FxxLW motif peptide


Mass: 2123.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Derived from phage display selections
#3: Chemical ChemComp-DHT / 5-ALPHA-DIHYDROTESTOSTERONE / Dihydrotestosterone


Mass: 290.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H30O2 / Comment: hormone*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 1.9 Å3/Da / Density % sol: 34.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: sodium citrate, TRIS, HEPES, lithium sulfate, glycerol, TCEP, n-octyl glucoside, 5-alpha dihydrotestosterone, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.12713 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 31, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 23860 / Num. obs: 23860 / % possible obs: 99 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.1 Å2 / Rsym value: 0.084 / Net I/σ(I): 19.1
Reflection shellResolution: 1.8→1.83 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.596 / % possible all: 89.6

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1217201.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1152 4.8 %RANDOM
Rwork0.2 ---
all-23771 --
obs-23771 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.5675 Å2 / ksol: 0.379274 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-14.44 Å20 Å20 Å2
2---7.91 Å20 Å2
3----6.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 21 145 2280
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.8355
X-RAY DIFFRACTIONc_improper_angle_d0.78993
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.332 188 5.1 %
Rwork0.299 3476 -
obs-3664 93.7 %
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 DIFFRACTION4DHT_LIGAND.PARDHT_LIGAND.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