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- PDB-7y04: Hsp90-AhR-p23 complex -

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Basic information

Entry
Database: PDB / ID: 7y04
TitleHsp90-AhR-p23 complex
Components
  • Aryl hydrocarbon receptor
  • Heat shock protein HSP 90-beta
  • Prostaglandin E synthase 3
KeywordsCYTOSOLIC PROTEIN / Hsp90 / AhR / complex / p23
Function / homology
Function and homology information


circumferential growth involved in left ventricle morphogenesis / negative regulation of calcium ion transmembrane transport / cellular response to 3-methylcholanthrene / regulation of heart growth / ESR-mediated signaling / cytosolic aryl hydrocarbon receptor complex / glomerulus morphogenesis / gland development / DDX58/IFIH1-mediated induction of interferon-alpha/beta / The NLRP3 inflammasome ...circumferential growth involved in left ventricle morphogenesis / negative regulation of calcium ion transmembrane transport / cellular response to 3-methylcholanthrene / regulation of heart growth / ESR-mediated signaling / cytosolic aryl hydrocarbon receptor complex / glomerulus morphogenesis / gland development / DDX58/IFIH1-mediated induction of interferon-alpha/beta / The NLRP3 inflammasome / HSF1-dependent transactivation / Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling / HSF1 activation / kidney morphogenesis / lung saccule development / RHOBTB2 GTPase cycle / Sema3A PAK dependent Axon repulsion / omega-hydroxylase P450 pathway / prostaglandin-E synthase / prostaglandin-E synthase activity / arachidonate omega-hydroxylase activity / ooplasm / positive regulation of growth rate / Attenuation phase / regulation of adaptive immune response / lymphocyte homeostasis / reactive oxygen species biosynthetic process / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / negative regulation of complement-dependent cytotoxicity / telomerase activity / Endogenous sterols / nuclear aryl hydrocarbon receptor complex / HSP90-CDC37 chaperone complex / reproductive structure development / receptor ligand inhibitor activity / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / nuclear receptor-mediated glucocorticoid signaling pathway / sperm head plasma membrane / The role of GTSE1 in G2/M progression after G2 checkpoint / cardiac left ventricle morphogenesis / negative regulation of proteasomal protein catabolic process / prostate gland development / negative regulation of osteoblast proliferation / negative regulation of T cell mediated immune response to tumor cell / aryl hydrocarbon receptor complex / Regulation of actin dynamics for phagocytic cup formation / dynein axonemal particle / histone methyltransferase binding / B-1 B cell homeostasis / Estrogen-dependent gene expression / cellular response to toxic substance / COP9 signalosome / post-embryonic hemopoiesis / negative regulation of DNA biosynthetic process / ATP-dependent protein binding / positive regulation of protein localization to cell surface / vasculature development / camera-type eye development / glycogen biosynthetic process / negative regulation of systemic arterial blood pressure / telomerase holoenzyme complex / blood circulation / protein folding chaperone complex / blood vessel morphogenesis / negative regulation of protein metabolic process / dATP binding / prostaglandin biosynthetic process / sulfonylurea receptor binding / CTP binding / UTP binding / heterocyclic compound binding / negative regulation of vasoconstriction / telomerase holoenzyme complex assembly / prostaglandin metabolic process / skin development / branching involved in blood vessel morphogenesis / immune system process / TPR domain binding / blood vessel development / T cell homeostasis / positive regulation of transforming growth factor beta receptor signaling pathway / B cell homeostasis / E-box binding / dendritic growth cone / aryl hydrocarbon receptor binding / chaperone cofactor-dependent protein refolding / regulation of protein ubiquitination / telomere maintenance via telomerase / positive regulation of cell size / protein localization to nucleus / chaperone-mediated protein complex assembly / blood vessel remodeling / positive regulation of RNA polymerase II transcription preinitiation complex assembly / negative regulation of osteoblast differentiation / toxic substance binding / cellular response to interleukin-4 / cis-regulatory region sequence-specific DNA binding
Similarity search - Function
Aryl hydrocarbon receptor / Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / Co-chaperone protein p23-like / CS domain / CS domain / CS domain profile. / PAS fold-3 / PAS fold / HSP20-like chaperone / Helix-loop-helix DNA-binding domain ...Aryl hydrocarbon receptor / Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / Co-chaperone protein p23-like / CS domain / CS domain / CS domain profile. / PAS fold-3 / PAS fold / HSP20-like chaperone / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / 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 / Histidine kinase-like ATPases / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / Heat shock protein HSP 90-beta / Aryl hydrocarbon receptor / Prostaglandin E synthase 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWen, Z.L. / Zhai, Y.J. / Zhu, Y. / Sun, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2023
Title: Cryo-EM structure of the cytosolic AhR complex.
Authors: Zuoling Wen / Yuebin Zhang / Beirong Zhang / Yumo Hang / Li Xu / Yangsheng Chen / Qunhui Xie / Qun Zhao / Lihua Zhang / Guohui Li / Bin Zhao / Fei Sun / Yujia Zhai / Yun Zhu /
Abstract: Aryl hydrocarbon receptor (AhR) is an important ligand-activated transcription factor involved in the regulation of various important physiological functions. Here, we report the cryo-EM structures ...Aryl hydrocarbon receptor (AhR) is an important ligand-activated transcription factor involved in the regulation of various important physiological functions. Here, we report the cryo-EM structures of the Hsp90-AhR-p23 complex with or without bound XAP2, where the structure of the mouse AhR PAS-B domain is resolved. A highly conserved bridge motif of AhR is responsible for the interaction with the Hsp90 dimeric lumen. The ligand-free AhR PAS-B domain is attached to the Hsp90 dimer and is stabilized in the complex with bound XAP2. In addition, the DE-loop and a group of conserved pocket inner residues in the AhR PAS-B domain are found to be important for ligand binding. These results reveal the structural basis of the biological functions of AhR. Moreover, the protein purification method presented here allows the isolation of stable mouse AhR protein, which could be used to develop high-sensitivity biosensors for environmental pollutant detection.
History
DepositionJun 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 4, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_DOI
Revision 1.2Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Mar 22, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.4Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein HSP 90-beta
B: Heat shock protein HSP 90-beta
C: Prostaglandin E synthase 3
D: Prostaglandin E synthase 3
E: Aryl hydrocarbon receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,5749
Polymers259,5885
Non-polymers9864
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Heat shock protein HSP 90-beta / Heat shock 84 kDa / HSP 84 / HSP84 / Tumor-specific transplantation 84 kDa antigen / TSTA


Mass: 86590.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hsp90ab1, Hsp84, Hsp84-1, Hspcb / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11499
#2: Protein Prostaglandin E synthase 3 / Cytosolic prostaglandin E2 synthase / cPGES / Hsp90 co-chaperone / Progesterone receptor complex ...Cytosolic prostaglandin E2 synthase / cPGES / Hsp90 co-chaperone / Progesterone receptor complex p23 / Sid 3177 / Telomerase-binding protein p23


Mass: 20133.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptges3, Sid3177, Tebp / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9R0Q7, prostaglandin-E synthase
#3: Protein Aryl hydrocarbon receptor


Mass: 46138.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P30561
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails
1Hsp90-AhR-p23 complexCOMPLEX#1-#30RECOMBINANT
2Heat shock protein HSP 90-betaCOMPLEX#11RECOMBINANT
3Prostaglandin E synthase 3COMPLEX#21RECOMBINANTalso named p23
4Aryl hydrocarbon receptorCOMPLEX#31RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Mus musculus (house mouse)10090
32Mus musculus (house mouse)10090
43Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Spodoptera frugiperda (fall armyworm)7108
32Spodoptera frugiperda (fall armyworm)7108
43Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 291578 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00212253
ELECTRON MICROSCOPYf_angle_d0.54116495
ELECTRON MICROSCOPYf_dihedral_angle_d4.881599
ELECTRON MICROSCOPYf_chiral_restr0.0431810
ELECTRON MICROSCOPYf_plane_restr0.0042105

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