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- EMDB-34519: Hsp90-AhR-p23-XAP2 complex -

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Entry
Database: EMDB / ID: EMD-34519
TitleHsp90-AhR-p23-XAP2 complex
Map data
Sample
  • Complex: mouse Hsp90-AhR-p23-XAP2 complex
    • Complex: Heat shock protein HSP 90-beta
      • Protein or peptide: Heat shock protein HSP 90-beta
    • Complex: Prostaglandin E synthase 3
      • Protein or peptide: Prostaglandin E synthase 3
    • Complex: Aryl hydrocarbon receptor
      • Protein or peptide: Aryl hydrocarbon receptor
    • Complex: AH receptor-interacting protein
      • Protein or peptide: AH receptor-interacting protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
KeywordsHsp90 / AhR / PASB doamin / complex / p23 / XAP2 / CYTOSOLIC PROTEIN
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 / GAF domain binding / ESR-mediated signaling / cytosolic aryl hydrocarbon receptor complex / glomerulus morphogenesis / gland development / DDX58/IFIH1-mediated induction of interferon-alpha/beta ...circumferential growth involved in left ventricle morphogenesis / negative regulation of calcium ion transmembrane transport / cellular response to 3-methylcholanthrene / regulation of heart growth / GAF domain binding / 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 / regulation of protein kinase A signaling / 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 / protein targeting to mitochondrion / 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 / protein maturation by protein folding / 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
Similarity search - Function
Aryl hydrocarbon receptor / Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / AIP/AIPL1 / Co-chaperone protein p23-like / CS domain / CS domain / CS domain profile. / PAS fold-3 / PAS fold / HSP20-like chaperone ...Aryl hydrocarbon receptor / Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / AIP/AIPL1 / 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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / 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 / TPR repeat region circular profile. / TPR repeat profile. / PAS fold / PAS fold / PAS domain / Tetratricopeptide repeat / PAS repeat profile. / PAS domain / Histidine kinase-like ATPases / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
AH receptor-interacting protein / 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: 3.2 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
DepositionOct 19, 2022-
Header (metadata) releaseJan 4, 2023-
Map releaseJan 4, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34519.png

Downloads & links

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Map

FileDownload / File: emd_34519.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.13686371 - 0.19737948
Average (Standard dev.)0.00015308852 (±0.0038646278)
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_34519_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_34519_half_map_2.map
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Sample components

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Entire : mouse Hsp90-AhR-p23-XAP2 complex

EntireName: mouse Hsp90-AhR-p23-XAP2 complex
Components
  • Complex: mouse Hsp90-AhR-p23-XAP2 complex
    • Complex: Heat shock protein HSP 90-beta
      • Protein or peptide: Heat shock protein HSP 90-beta
    • Complex: Prostaglandin E synthase 3
      • Protein or peptide: Prostaglandin E synthase 3
    • Complex: Aryl hydrocarbon receptor
      • Protein or peptide: Aryl hydrocarbon receptor
    • Complex: AH receptor-interacting protein
      • Protein or peptide: AH receptor-interacting protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION

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Supramolecule #1: mouse Hsp90-AhR-p23-XAP2 complex

SupramoleculeName: mouse Hsp90-AhR-p23-XAP2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: Heat shock protein HSP 90-beta

SupramoleculeName: Heat shock protein HSP 90-beta / type: complex / ID: 2 / 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 / 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 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #5: AH receptor-interacting protein

SupramoleculeName: AH receptor-interacting protein / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4 / Details: also named AIP, XAP2
Source (natural)Organism: Mus musculus (house mouse)

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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

UniProtKB: Heat shock protein HSP 90-beta

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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

UniProtKB: Prostaglandin E synthase 3

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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: 50.507441 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 TSLPFMFATG EAVLYEISSP FSPIMDPLPI RTKSNTSRKD WAPQ

UniProtKB: Aryl hydrocarbon receptor

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Macromolecule #4: AH receptor-interacting protein

MacromoleculeName: AH receptor-interacting protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 38.744102 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAYPYDVPDY ADLIARLRED GIQKRVIQEG RGELPDFQDG TKATFHFRTL HSDNEGSVID DSRTRGKPME LIVGKKFKLP VWETIVCTM REGEIAQFLC DIKHVVLYPL VAKSLRNIAE GKDPLEGQRH CCGIAQMHEH SSLGHADLDA LQQNPQPLIF H IEMLKVES ...String:
MAYPYDVPDY ADLIARLRED GIQKRVIQEG RGELPDFQDG TKATFHFRTL HSDNEGSVID DSRTRGKPME LIVGKKFKLP VWETIVCTM REGEIAQFLC DIKHVVLYPL VAKSLRNIAE GKDPLEGQRH CCGIAQMHEH SSLGHADLDA LQQNPQPLIF H IEMLKVES PGTYQQDPWA MTDEEKAKAV PVIHQEGNRL YREGQVKEAA AKYYDAIACL KNLQMKEQPG SPDWIQLDLQ IT PLLLNYC QCKLVAQEYY EVLDHCSSIL NKYDDNVKAY FKRGKAHAAV WNAQEAQADF AKVLELDPAL APVVSRELRA LET RIRQKD EEDKARFRGI FSH

UniProtKB: AH receptor-interacting protein

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

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

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

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Macromolecule #6: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 6 / 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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 266830
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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