[English] 日本語
Yorodumi
- PDB-5v0l: Crystal structure of the AHR-ARNT heterodimer in complex with the DRE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v0l
TitleCrystal structure of the AHR-ARNT heterodimer in complex with the DRE
Components
  • (Aryl hydrocarbon ...) x 2
  • DNA (5'-D(P*AP*GP*TP*TP*CP*TP*CP*AP*CP*GP*CP*AP*AP*T)-3')
  • DNA (5'-D(P*GP*GP*AP*TP*TP*GP*CP*GP*TP*GP*AP*GP*AP*AP*CP*TP*G)-3')
KeywordsTRANSCRIPTION/DNA / AHR / ARNT / transcription factor / heterodimer / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


circumferential growth involved in left ventricle morphogenesis / positive regulation of mating-type specific transcription, DNA-templated / negative regulation of calcium ion transmembrane transport / cellular response to 3-methylcholanthrene / cytosolic aryl hydrocarbon receptor complex / glomerulus morphogenesis / gland development / regulation of heart growth / regulation of eating behavior / Xenobiotics ...circumferential growth involved in left ventricle morphogenesis / positive regulation of mating-type specific transcription, DNA-templated / negative regulation of calcium ion transmembrane transport / cellular response to 3-methylcholanthrene / cytosolic aryl hydrocarbon receptor complex / glomerulus morphogenesis / gland development / regulation of heart growth / regulation of eating behavior / Xenobiotics / Aryl hydrocarbon receptor signalling / regulation of B cell proliferation / Phase I - Functionalization of compounds / kidney morphogenesis / arachidonate omega-hydroxylase activity / omega-hydroxylase P450 pathway / contact inhibition / positive regulation of growth rate / reactive oxygen species biosynthetic process / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / Endogenous sterols / lymphocyte homeostasis / negative regulation of DNA biosynthetic process / regulation of adaptive immune response / nuclear aryl hydrocarbon receptor complex / mammary duct terminal end bud growth / cardiac left ventricle morphogenesis / negative regulation of osteoblast proliferation / positive regulation of hormone biosynthetic process / Aryl hydrocarbon receptor signalling / prostate gland development / cellular response to molecule of bacterial origin / reproductive structure development / aryl hydrocarbon receptor complex / B-1 B cell homeostasis / positive regulation of protein sumoylation / negative regulation of T cell mediated immune response to tumor cell / intestinal epithelial structure maintenance / post-embryonic hemopoiesis / Xenobiotics / camera-type eye development / conditioned taste aversion / Phase I - Functionalization of compounds / cellular response to toxic substance / vasculature development / blood vessel morphogenesis / positive regulation of vascular endothelial growth factor receptor signaling pathway / Regulation of gene expression by Hypoxia-inducible Factor / negative regulation of systemic arterial blood pressure / negative regulation of vasoconstriction / blood circulation / branching involved in blood vessel morphogenesis / blood vessel development / E-box binding / aryl hydrocarbon receptor binding / B cell homeostasis / T cell homeostasis / TFIID-class transcription factor complex binding / positive regulation of cell size / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of vascular endothelial growth factor production / Endogenous sterols / blood vessel remodeling / embryonic placenta development / negative regulation of osteoblast differentiation / immune system process / toxic substance binding / protein localization to nucleus / ovarian follicle development / cis-regulatory region sequence-specific DNA binding / spleen development / estrogen receptor signaling pathway / NPAS4 regulates expression of target genes / positive regulation of endothelial cell proliferation / xenobiotic metabolic process / regulation of cytokine production / positive regulation of erythrocyte differentiation / B cell differentiation / TBP-class protein binding / cellular response to cAMP / positive regulation of glycolytic process / cellular response to forskolin / circadian regulation of gene expression / promoter-specific chromatin binding / liver development / PPARA activates gene expression / Hsp90 protein binding / nuclear receptor activity / negative regulation of inflammatory response / transcription coactivator binding / RNA polymerase II transcription regulator complex / response to toxic substance / cell morphogenesis / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / protein-folding chaperone binding / regulation of gene expression / cellular response to oxidative stress / transcription regulator complex / transcription by RNA polymerase II
Similarity search - Function
Aryl hydrocarbon receptor / Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / : / Nuclear translocator / PAS fold-3 / PAS fold / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain ...Aryl hydrocarbon receptor / Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / : / Nuclear translocator / PAS fold-3 / PAS fold / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
CITRIC ACID / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / Aryl hydrocarbon receptor nuclear translocator / Aryl hydrocarbon receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsSeok, S.-H. / Lee, W. / Jiang, L. / Bradfield, C.A. / Xing, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM096060-01 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural hierarchy controlling dimerization and target DNA recognition in the AHR transcriptional complex.
Authors: Seok, S.H. / Lee, W. / Jiang, L. / Molugu, K. / Zheng, A. / Li, Y. / Park, S. / Bradfield, C.A. / Xing, Y.
History
DepositionFeb 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2Jun 7, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aryl hydrocarbon receptor nuclear translocator
B: Aryl hydrocarbon receptor
C: DNA (5'-D(P*GP*GP*AP*TP*TP*GP*CP*GP*TP*GP*AP*GP*AP*AP*CP*TP*G)-3')
D: DNA (5'-D(P*AP*GP*TP*TP*CP*TP*CP*AP*CP*GP*CP*AP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3248
Polymers67,7274
Non-polymers5964
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-52 kcal/mol
Surface area27140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.199, 64.364, 157.725
Angle α, β, γ (deg.)90.00, 100.14, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Aryl hydrocarbon ... , 2 types, 2 molecules AB

#1: Protein Aryl hydrocarbon receptor nuclear translocator / ARNT protein / Class E basic helix-loop-helix protein 2 / bHLHe2 / Dioxin receptor / nuclear ...ARNT protein / Class E basic helix-loop-helix protein 2 / bHLHe2 / Dioxin receptor / nuclear translocator / Hypoxia-inducible factor 1-beta / HIF1-beta


Mass: 31028.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARNT, BHLHE2 / Plasmid: pQLinkH
Details (production host): Vectors for co-expression of proteins
Production host: Escherichia coli (E. coli) / References: UniProt: P27540
#2: Protein Aryl hydrocarbon receptor / AhR


Mass: 27151.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ahr / Plasmid: pQLinkH
Details (production host): Vectors for co-expression of proteins
Production host: Escherichia coli (E. coli) / References: UniProt: P30561

-
DNA chain , 2 types, 2 molecules CD

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


Mass: 5307.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(P*AP*GP*TP*TP*CP*TP*CP*AP*CP*GP*CP*AP*AP*T)-3')


Mass: 4239.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 277 K / Method: evaporation
Details: 10%-12% PEG 20000, 4-6% Tacsimate pH 7.0 or 0.1 M Bis-Tris pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 12, 2016
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. obs: 6690 / % possible obs: 99.5 % / Redundancy: 7.9 % / Rpim(I) all: 0.075 / Net I/σ(I): 11
Reflection shellResolution: 3.9→3.97 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 669 / Rpim(I) all: 0.592 / % possible all: 96

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZPK

4zpk


Resolution: 4→39.685 Å / SU ML: 0.72 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 46.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3226 332 4.98 %
Rwork0.2852 --
obs0.2872 6660 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4→39.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2738 640 40 0 3418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023594
X-RAY DIFFRACTIONf_angle_d0.6714971
X-RAY DIFFRACTIONf_dihedral_angle_d15.5072051
X-RAY DIFFRACTIONf_chiral_restr0.087559
X-RAY DIFFRACTIONf_plane_restr0.003527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0001-5.03810.4331640.35313143X-RAY DIFFRACTION100
5.0381-39.68670.29411680.26573185X-RAY DIFFRACTION99

+
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