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- EMDB-14971: Cryo-EM structure of the indirubin-bound Hsp90-XAP2-AHR complex -

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Basic information

Entry
Database: EMDB / ID: EMD-14971
TitleCryo-EM structure of the indirubin-bound Hsp90-XAP2-AHR complex
Map data
Sample
  • Complex: Hsp90-XAP2-AHR complex
    • Protein or peptide: Heat shock protein HSP 90-beta
    • Protein or peptide: AH receptor-interacting protein
    • Protein or peptide: Aryl hydrocarbon receptor
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: MOLYBDATE ION
  • Ligand: (3~{Z})-3-(3-oxidanylidene-1~{H}-indol-2-ylidene)-1~{H}-indol-2-one
Function / homology
Function and homology information


GAF domain binding / negative regulation of T cell mediated immune response to tumor cell / cytosolic aryl hydrocarbon receptor complex / regulation of B cell proliferation / cellular response to molecule of bacterial origin / regulation of adaptive immune response / : / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / nuclear aryl hydrocarbon receptor complex / HSP90-CDC37 chaperone complex ...GAF domain binding / negative regulation of T cell mediated immune response to tumor cell / cytosolic aryl hydrocarbon receptor complex / regulation of B cell proliferation / cellular response to molecule of bacterial origin / regulation of adaptive immune response / : / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / nuclear aryl hydrocarbon receptor complex / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / dynein axonemal particle / histone methyltransferase binding / regulation of protein kinase A signaling / Xenobiotics / positive regulation of protein localization to cell surface / protein targeting to mitochondrion / ATP-dependent protein binding / protein kinase regulator activity / Phase I - Functionalization of compounds / protein maturation by protein folding / negative regulation of protein metabolic process / positive regulation of tau-protein kinase activity / telomerase holoenzyme complex assembly / Respiratory syncytial virus genome replication / Uptake and function of diphtheria toxin / TPR domain binding / blood vessel development / positive regulation of transforming growth factor beta receptor signaling pathway / Assembly and release of respiratory syncytial virus (RSV) virions / E-box binding / dendritic growth cone / positive regulation of phosphoprotein phosphatase activity / TFIID-class transcription factor complex binding / aryl hydrocarbon receptor binding / Sema3A PAK dependent Axon repulsion / The NLRP3 inflammasome / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / telomere maintenance via telomerase / chaperone-mediated protein complex assembly / HSF1 activation / Attenuation phase / cellular response to interleukin-4 / Endogenous sterols / RHOBTB2 GTPase cycle / cis-regulatory region sequence-specific DNA binding / Purinergic signaling in leishmaniasis infection / axonal growth cone / DNA polymerase binding / supramolecular fiber organization / cellular response to cAMP / cellular response to forskolin / positive regulation of telomerase activity / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / TBP-class protein binding / nitric-oxide synthase regulator activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / xenobiotic metabolic process / cAMP-mediated signaling / ESR-mediated signaling / peptidyl-prolyl cis-trans isomerase activity / positive regulation of cell differentiation / ATP-dependent protein folding chaperone / peptide binding / circadian regulation of gene expression / Hsp90 protein binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / placenta development / tau protein binding / PPARA activates gene expression / response to toxic substance / Regulation of actin dynamics for phagocytic cup formation / transcription coactivator binding / kinase binding / negative regulation of inflammatory response / histone deacetylase binding / Chaperone Mediated Autophagy / The role of GTSE1 in G2/M progression after G2 checkpoint / nuclear receptor activity / regulation of protein localization / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / double-stranded RNA binding / disordered domain specific binding / unfolded protein binding / melanosome / protein folding / MHC class II protein complex binding / cellular response to heat / regulation of gene expression / secretory granule lumen / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding
Similarity search - Function
Aryl hydrocarbon receptor / Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / AIP/AIPL1 / 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) / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. ...Aryl hydrocarbon receptor / Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / AIP/AIPL1 / 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) / 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 profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / 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. / 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
AH receptor-interacting protein / Heat shock protein HSP 90-beta / Aryl hydrocarbon receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsGruszczyk J / Savva CG / Lai-Kee-Him J / Bous J / Ancelin A / Kwong HS / Grandvuillemin L / Bourguet W
Funding supportEuropean Union, France, 3 items
OrganizationGrant numberCountry
European Union (EU)825489European Union
ATIP-AvenirR20059SP France
Montpellier University of Excellence (MUSE)ANR-16-IDEX-0006 France
CitationJournal: Nat Commun / Year: 2022
Title: Cryo-EM structure of the agonist-bound Hsp90-XAP2-AHR cytosolic complex.
Authors: Jakub Gruszczyk / Loïc Grandvuillemin / Josephine Lai-Kee-Him / Matteo Paloni / Christos G Savva / Pierre Germain / Marina Grimaldi / Abdelhay Boulahtouf / Hok-Sau Kwong / Julien Bous / ...Authors: Jakub Gruszczyk / Loïc Grandvuillemin / Josephine Lai-Kee-Him / Matteo Paloni / Christos G Savva / Pierre Germain / Marina Grimaldi / Abdelhay Boulahtouf / Hok-Sau Kwong / Julien Bous / Aurélie Ancelin / Cherine Bechara / Alessandro Barducci / Patrick Balaguer / William Bourguet /
Abstract: The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that mediates a broad spectrum of (patho)physiological processes in response to numerous substances including ...The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that mediates a broad spectrum of (patho)physiological processes in response to numerous substances including pollutants, natural products and metabolites. However, the scarcity of structural data precludes understanding of how AHR is activated by such diverse compounds. Our 2.85 Å structure of the human indirubin-bound AHR complex with the chaperone Hsp90 and the co-chaperone XAP2, reported herein, reveals a closed conformation Hsp90 dimer with AHR threaded through its lumen and XAP2 serving as a brace. Importantly, we disclose the long-awaited structure of the AHR PAS-B domain revealing a unique organisation of the ligand-binding pocket and the structural determinants of ligand-binding specificity and promiscuity of the receptor. By providing structural details of the molecular initiating event leading to AHR activation, our study rationalises almost forty years of biochemical data and provides a framework for future mechanistic studies and structure-guided drug design.
History
DepositionMay 12, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateDec 7, 2022-
Current statusDec 7, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14971.png

Downloads & links

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Map

FileDownload / File: emd_14971.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.086 Å
Density
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.09270059 - 0.33115554
Average (Standard dev.)0.0001130128 (±0.0026355188)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 347.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14971_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_14971_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_14971_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Hsp90-XAP2-AHR complex

EntireName: Hsp90-XAP2-AHR complex
Components
  • Complex: Hsp90-XAP2-AHR complex
    • Protein or peptide: Heat shock protein HSP 90-beta
    • Protein or peptide: AH receptor-interacting protein
    • Protein or peptide: Aryl hydrocarbon receptor
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: MOLYBDATE ION
  • Ligand: (3~{Z})-3-(3-oxidanylidene-1~{H}-indol-2-ylidene)-1~{H}-indol-2-one

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Supramolecule #1: Hsp90-XAP2-AHR complex

SupramoleculeName: Hsp90-XAP2-AHR complex / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 256 KDa

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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: Homo sapiens (human)
Molecular weightTheoretical: 84.213141 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHPEE VHHGEEEVET FAFQAEIAQL MSLIINTFYS NKEIFLRELI SNASDALDKI RYESLTDPSK LDSGKELKID IIPNPQERT LTLVDTGIGM TKADLINNLG TIAKSGTKAF MEALQAGADI SMIGQFGVGF YSAYLVAEKV VVITKHNDDE Q YAWESSAG ...String:
MHHHHHHPEE VHHGEEEVET FAFQAEIAQL MSLIINTFYS NKEIFLRELI SNASDALDKI RYESLTDPSK LDSGKELKID IIPNPQERT LTLVDTGIGM TKADLINNLG TIAKSGTKAF MEALQAGADI SMIGQFGVGF YSAYLVAEKV VVITKHNDDE Q YAWESSAG GSFTVRADHG EPIGRGTKVI LHLKEDQTEY LEERRVKEVV KKHSQFIGYP ITLYLEKERE KEISDDEAEE EK GEKEEED KDDEEKPKIE DVGSDEEDDS GKDKKKKTKK IKEKYIDQEE LNKTKPIWTR NPDDITQEEY GEFYKSLTND WED HLAVKH FSVEGQLEFR ALLFIPRRAP FDLFENKKKK NNIKLYVRRV FIMDSCDELI PEYLNFIRGV VDSEDLPLNI SREM LQQSK ILKVIRKNIV KKCLELFSEL AEDKENYKKF YEAFSKNLKL GIHEDSTNRR RLSELLRYHT SQSGDEMTSL SEYVS RMKE TQKSIYYITG ESKEQVANSA FVERVRKRGF EVVYMTEPID EYCVQQLKEF DGKSLVSVTK EGLELPEDEE EKKKME ESK AKFENLCKLM KEILDKKVEK VTISNRLVSS PCCIVTSTYG WTANMERIMK AQALRDNSTM GYMMAKKHLE INPDHPI VE TLRQKAEADK NDKAVKDLVV LLFETALLSS GFSLEDPQTH SNRIYRMIKL GLGIDEDEVA AEEPNAAVPD EIPPLEGD E DASRMEEVD

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Macromolecule #2: AH receptor-interacting protein

MacromoleculeName: AH receptor-interacting protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.691047 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MADIIARLRE DGIQKRVIQE GRGELPDFQD GTKATFHYRT LHSDDEGTVL DDSRARGKPM ELIIGKKFKL PVWETIVCTM REGEIAQFL CDIKHVVLYP LVAKSLRNIA VGKDPLEGQR HCCGVAQMRE HSSLGHADLD ALQQNPQPLI FHMEMLKVES P GTYQQDPW ...String:
MADIIARLRE DGIQKRVIQE GRGELPDFQD GTKATFHYRT LHSDDEGTVL DDSRARGKPM ELIIGKKFKL PVWETIVCTM REGEIAQFL CDIKHVVLYP LVAKSLRNIA VGKDPLEGQR HCCGVAQMRE HSSLGHADLD ALQQNPQPLI FHMEMLKVES P GTYQQDPW AMTDEEKAKA VPLIHQEGNR LYREGHVKEA AAKYYDAIAC LKNLQMKEQP GSPEWIQLDQ QITPLLLNYC QC KLVVEEY YEVLDHCSSI LNKYDDNVKA YFKRGKAHAA VWNAQEAQAD FAKVLELDPA LAPVVSRELQ ALEARIRQKD EED KARFRG IFSH

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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: Homo sapiens (human)
Molecular weightTheoretical: 49.767879 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: APNSMNSSSA NITYASRKRR KPVQKTVKPI PAEGIKSNPS KRHRDRLNTE LDRLASLLPF PQDVINKLDK LSVLRLSVSY LRAKSFFDV ALKSSPTERN GGQDNCRAAN FREGLNLQEG EFLLQALNGF VLVVTTDALV FYASSTIQDY LGFQQSDVIH Q SVYELIHT ...String:
APNSMNSSSA NITYASRKRR KPVQKTVKPI PAEGIKSNPS KRHRDRLNTE LDRLASLLPF PQDVINKLDK LSVLRLSVSY LRAKSFFDV ALKSSPTERN GGQDNCRAAN FREGLNLQEG EFLLQALNGF VLVVTTDALV FYASSTIQDY LGFQQSDVIH Q SVYELIHT EDRAEFQRQL HWALNPSQCT ESGQGIEEAT GLPQTVVCYN PDQIPPENSP LMERCFICRL RCLLDNSSGF LA MNFQGKL KYLHGQKKKG KDGSILPPQL ALFAIATPLQ PPSILEIRTK NFIFRTKHKL DFTPIGCDAK GRIVLGYTEA ELC TRGSGY QFIHAADMLY CAESHIRMIK TGESGMIVFR LLTKNNRWTW VQSNARLLYK NGRPDYIIVT QRPLTDEEGT EHLR KRNTK LPFMFTTGEA VLYEATNPFP AIMDPLPLRT KNGTSG

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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

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: MOLYBDATE ION

MacromoleculeName: MOLYBDATE ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MOO
Molecular weightTheoretical: 159.938 Da
Chemical component information

ChemComp-MOO:
MOLYBDATE ION

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Macromolecule #7: (3~{Z})-3-(3-oxidanylidene-1~{H}-indol-2-ylidene)-1~{H}-indol-2-one

MacromoleculeName: (3~{Z})-3-(3-oxidanylidene-1~{H}-indol-2-ylidene)-1~{H}-indol-2-one
type: ligand / ID: 7 / Number of copies: 1 / Formula: JY6
Molecular weightTheoretical: 262.263 Da
Chemical component information

ChemComp-JY6:
(3~{Z})-3-(3-oxidanylidene-1~{H}-indol-2-ylidene)-1~{H}-indol-2-one

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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

Concentration0.2 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
20.0 mMBis-Trisbis-tris methane
50.0 mMNaClsodium chloride
10.0 mMKClpotassium chloride
10.0 mMMgCl2magnesium chloride
20.0 mMNa2MoO4sodium molybdate
2.0 mMBME2-mercaptoethanol
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 20.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 9300 / Average exposure time: 3.0 sec. / Average electron dose: 1.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 11546649
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model generated with RELION
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 678724
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final 3D classificationNumber classes: 1 / Avg.num./class: 678724 / Software - Name: RELION (ver. 3.1.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

5fwp

,

4f3l

,

4zpr

,

2lkn

,

4aif

)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7zub:
Cryo-EM structure of the indirubin-bound Hsp90-XAP2-AHR complex

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