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- EMDB-33537: Hsp90-AhR-p23 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-33537
TitleHsp90-AhR-p23 complex
Map dataHsp90-AhR-p23 complex
Sample
  • Complex: Hsp90-AhR-p23 complex
    • Complex: Heat shock protein HSP 90-betaHeat shock response
      • Protein or peptide: Heat shock protein HSP 90-betaHeat shock response
    • Complex: Prostaglandin E synthase 3
      • Protein or peptide: Prostaglandin E synthase 3
    • Complex: Aryl hydrocarbon receptor
      • Protein or peptide: Aryl hydrocarbon receptor
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
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 / negative regulation of T cell mediated immune response to tumor cell / cytosolic aryl hydrocarbon receptor complex / glomerulus morphogenesis / 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 / negative regulation of T cell mediated immune response to tumor cell / cytosolic aryl hydrocarbon receptor complex / glomerulus morphogenesis / DDX58/IFIH1-mediated induction of interferon-alpha/beta / The NLRP3 inflammasome / gland development / HSF1-dependent transactivation / regulation of B cell proliferation / reactive oxygen species biosynthetic process / Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling / HSF1 activation / kidney morphogenesis / RHOBTB2 GTPase cycle / lung saccule development / cellular response to molecule of bacterial origin / ooplasm / omega-hydroxylase P450 pathway / Sema3A PAK dependent Axon repulsion / prostaglandin-E synthase / prostaglandin-E synthase activity / arachidonic acid omega-hydroxylase activity / central nervous system neuron axonogenesis / positive regulation of growth rate / lymphocyte homeostasis / Attenuation phase / regulation of adaptive immune response / : / : / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / negative regulation of complement-dependent cytotoxicity / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / telomerase activity / Endogenous sterols / nuclear aryl hydrocarbon receptor complex / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / intracellular glucocorticoid receptor signaling pathway / cardiac left ventricle morphogenesis / The role of GTSE1 in G2/M progression after G2 checkpoint / sperm head plasma membrane / negative regulation of proteasomal protein catabolic process / negative regulation of osteoblast proliferation / cellular response to toxic substance / reproductive structure development / prostate gland development / aryl hydrocarbon receptor complex / dynein axonemal particle / Regulation of actin dynamics for phagocytic cup formation / histone methyltransferase binding / B-1 B cell homeostasis / Estrogen-dependent gene expression / post-embryonic hemopoiesis / COP9 signalosome / positive regulation of protein localization to cell surface / negative regulation of DNA biosynthetic process / ATP-dependent protein binding / camera-type eye development / vasculature development / axon extension / telomerase holoenzyme complex / negative regulation of systemic arterial blood pressure / glycogen biosynthetic process / protein folding chaperone complex / blood circulation / blood vessel morphogenesis / prostaglandin biosynthetic process / dATP binding / sulfonylurea receptor binding / CTP binding / negative regulation of protein metabolic process / skin development / UTP binding / negative regulation of vasoconstriction / branching involved in blood vessel morphogenesis / telomerase holoenzyme complex assembly / immune system process / establishment of cell polarity / prostaglandin metabolic process / heterocyclic compound binding / blood vessel development / TPR domain binding / E-box binding / T cell homeostasis / positive regulation of transforming growth factor beta receptor signaling pathway / dendritic growth cone / chaperone cofactor-dependent protein refolding / positive regulation of phosphoprotein phosphatase activity / TFIID-class transcription factor complex binding / aryl hydrocarbon receptor binding / B cell homeostasis / cAMP-mediated signaling / regulation of protein ubiquitination
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 / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Heat shock protein HSP 90-beta / Aryl hydrocarbon receptor / Prostaglandin E synthase 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWen ZL / Zhai YJ / Zhu Y / Sun F
Funding support1 items
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, 2022-
Header (metadata) releaseJan 4, 2023-
Map releaseJan 4, 2023-
UpdateMar 22, 2023-
Current statusMar 22, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33537.png

Downloads & links

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Map

FileDownload / File: emd_33537.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHsp90-AhR-p23 complex
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-3.1070776 - 5.1881504
Average (Standard dev.)-0.0013249167 (±0.10402255)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33537_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33537_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hsp90-AhR-p23 complex

EntireName: Hsp90-AhR-p23 complex
Components
  • Complex: Hsp90-AhR-p23 complex
    • Complex: Heat shock protein HSP 90-betaHeat shock response
      • Protein or peptide: Heat shock protein HSP 90-betaHeat shock response
    • Complex: Prostaglandin E synthase 3
      • Protein or peptide: Prostaglandin E synthase 3
    • Complex: Aryl hydrocarbon receptor
      • Protein or peptide: Aryl hydrocarbon receptor
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION

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Supramolecule #1: Hsp90-AhR-p23 complex

SupramoleculeName: Hsp90-AhR-p23 complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #2: Heat shock protein HSP 90-beta

SupramoleculeName: Heat shock protein HSP 90-beta / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: Prostaglandin E synthase 3

SupramoleculeName: Prostaglandin E synthase 3 / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #2 / Details: also named p23
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #4: Aryl hydrocarbon receptor

SupramoleculeName: Aryl hydrocarbon receptor / type: complex / ID: 4 / Chimera: Yes / Parent: 1 / Macromolecule list: #3

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Macromolecule #1: Heat shock protein HSP 90-beta

MacromoleculeName: Heat shock protein HSP 90-beta / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 86.590688 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGAWSHPQFE KGGGSGGGSG GGSAWSHPQF EKMPEEVHHG EEEVETFAFQ AEIAQLMSLI INTFYSNKEI FLRELISNAS DALDKIRYE SLTDPSKLDS GKELKIDIIP NPQERTLTLV DTGIGMTKAD LINNLGTIAK SGTKAFMEAL QAGADISMIG Q FGVGFYSA ...String:
MGAWSHPQFE KGGGSGGGSG GGSAWSHPQF EKMPEEVHHG EEEVETFAFQ AEIAQLMSLI INTFYSNKEI FLRELISNAS DALDKIRYE SLTDPSKLDS GKELKIDIIP NPQERTLTLV DTGIGMTKAD LINNLGTIAK SGTKAFMEAL QAGADISMIG Q FGVGFYSA YLVAEKVVVI TKHNDDEQYA WESSAGGSFT VRADHGEPIG RGTKVILHLK EDQTEYLEER RVKEVVKKHS QF IGYPITL YLEKEREKEI SDDEAEEEKG EKEEEDKEDE EKPKIEDVGS DEEDDSGKDK KKKTKKIKEK YIDQEELNKT KPI WTRNPD DITQEEYGEF YKSLTNDWED HLAVKHFSVE GQLEFRALLF IPRRAPFDLF ENKKKKNNIK LYVRRVFIMD SCDE LIPEY LNFIRGVVDS EDLPLNISRE MLQQSKILKV IRKNIVKKCL ELFSELAEDK ENYKKFYEAF SKNLKLGIHE DSTNR RRLS ELLRYHTSQS GDEMTSLSEY VSRMKETQKS IYYITGESKE QVANSAFVER VRKRGFEVVY MTEPIDEYCV QQLKEF DGK SLVSVTKEGL ELPEDEEEKK KMEESKAKFE NLCKLMKEIL DKKVEKVTIS NRLVSSPCCI VTSTYGWTAN MERIMKA QA LRDNSTMGYM MAKKHLEINP DHPIVETLRQ KAEADKNDKA VKDLVVLLFE TALLSSGFSL EDPQTHSNRI YRMIKLGL G IDEDEVTAEE PSAAVPDEIP PLEGDEDASR MEEVD

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Macromolecule #2: Prostaglandin E synthase 3

MacromoleculeName: Prostaglandin E synthase 3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: prostaglandin-E synthase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 20.133994 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MAEQKLISEE DLMQPASAKW YDRRDYVFIE FCVEDSKDVN VNFEKSKLTF SCLGGSDNFK HLNEIDLFHC IDPNDSKHKR TDRSILCCL RKGESGQSWP RLTKERAKLN WLSVDFNNWK DWEDDSDEDM SNFDRFSEMM DHMGGDEDVD LPEVDGADDD S QDSDDEKM PDLE

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Macromolecule #3: Aryl hydrocarbon receptor

MacromoleculeName: Aryl hydrocarbon receptor / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 46.138473 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPGASGGGSG AGMSSGANIT YASRKRRKPV QKTVKPIPAE GIKSNPSKRH RDRLNTELDR LASLLPFPQD VINKLDKLSV LRLSVSYLR AKSFFDVALK STPADRNGGQ DQCRAQIRDW QDLQEGEFLL QALNGFVLVV TADALVFYAS STIQDYLGFQ Q SDVIHQSV ...String:
GPGASGGGSG AGMSSGANIT YASRKRRKPV QKTVKPIPAE GIKSNPSKRH RDRLNTELDR LASLLPFPQD VINKLDKLSV LRLSVSYLR AKSFFDVALK STPADRNGGQ DQCRAQIRDW QDLQEGEFLL QALNGFVLVV TADALVFYAS STIQDYLGFQ Q SDVIHQSV YELIHTEDRA EFQRQLHWAL NPDSAQGVDE AHGPPQAAVY YTPDQLPPEN ASFMERCFRC RLRCLLDNSS GF LAMNFQG RLKYLHGQNK KGKDGALLPP QLALFAIATP LQPPSILEIR TKNFIFRTKH KLDFTPIGCD AKGQLILGYT EVE LCTRGS GYQFIHAADM LHCAESHIRM IKTGESGMTV FRLFAKHSRW RWVQSNARLI YRNGRPDYII ATQRPLTDEE GREH LQKRS TSLPF

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Macromolecule #5: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.3 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 291578
FSC plot (resolution estimation)

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