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- PDB-8h77: Hsp90-AhR-p23-XAP2 complex -

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Basic information

Entry
Database: PDB / ID: 8h77
TitleHsp90-AhR-p23-XAP2 complex
Components
  • AH receptor-interacting protein
  • Aryl hydrocarbon receptor
  • Heat shock protein HSP 90-betaHeat shock response
  • Prostaglandin E synthase 3
KeywordsCYTOSOLIC PROTEIN / Hsp90 / AhR / PASB doamin / complex / p23 / XAP2
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 / 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 ...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 / 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 cyclic-nucleotide phosphodiesterase activity / 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 / regulation of protein kinase A signaling / post-embryonic hemopoiesis / COP9 signalosome / protein targeting to mitochondrion / 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 / protein maturation by protein folding / 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
Similarity search - Function
AH receptor-interacting protein / Aryl hydrocarbon receptor / Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / Co-chaperone protein p23-like / AIP/AIPL1 / CS domain / CS domain / CS domain profile. / PAS fold-3 / PAS fold ...AH receptor-interacting protein / Aryl hydrocarbon receptor / Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / Co-chaperone protein p23-like / AIP/AIPL1 / 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 / 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 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. / TPR repeat region circular profile. / TPR repeat profile. / PAS fold / PAS fold / PAS domain / Tetratricopeptide repeat / 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 / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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
DepositionOct 19, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
F: AH receptor-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,68710
Polymers302,7016
Non-polymers9864
Water0
1


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

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Components

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Protein , 4 types, 6 molecules ABCDEF

#1: Protein Heat shock protein HSP 90-beta / Heat shock response / 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 / / Ah receptor / AhR


Mass: 50507.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ahr / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P30561
#4: Protein AH receptor-interacting protein / / AIP / Aryl-hydrocarbon receptor-interacting protein


Mass: 38744.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aip / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O08915

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Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


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


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

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Details

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
1mouse Hsp90-AhR-p23-XAP2 complexCOMPLEX#1-#40RECOMBINANT
2Heat shock protein HSP 90-betaHeat shock responseCOMPLEX#11RECOMBINANT
3Prostaglandin E synthase 3COMPLEX#21RECOMBINANTalso named p23
4Aryl hydrocarbon receptorCOMPLEX#31RECOMBINANT
5AH receptor-interacting proteinCOMPLEX#41RECOMBINANTalso named AIP, XAP2
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Mus musculus (house mouse)10090
33Mus musculus (house mouse)10090
44Mus musculus (house mouse)10090
55Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Spodoptera frugiperda (fall armyworm)7108
33Spodoptera frugiperda (fall armyworm)7108
44Spodoptera frugiperda (fall armyworm)7108
55Spodoptera 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 FIELDBright-field microscopy / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 266830 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00616028
ELECTRON MICROSCOPYf_angle_d0.7621575
ELECTRON MICROSCOPYf_dihedral_angle_d8.2972117
ELECTRON MICROSCOPYf_chiral_restr0.0462356
ELECTRON MICROSCOPYf_plane_restr0.0052766

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