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- PDB-8eoa: Cryo-EM structure of human HSP90B-AIPL1 complex -

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Basic information

Entry
Database: PDB / ID: 8eoa
TitleCryo-EM structure of human HSP90B-AIPL1 complex
Components
  • Aryl-hydrocarbon-interacting protein-like 1
  • Heat shock protein HSP 90-beta
KeywordsCHAPERONE / HSP90B / AIPL1 / phosphodiesterase 6
Function / homology
Function and homology information


farnesylated protein binding / HSP90-CDC37 chaperone complex / regulation of opsin-mediated signaling pathway / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / histone methyltransferase binding / dynein axonemal particle / receptor ligand inhibitor activity / protein kinase regulator activity ...farnesylated protein binding / HSP90-CDC37 chaperone complex / regulation of opsin-mediated signaling pathway / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / histone methyltransferase binding / dynein axonemal particle / receptor ligand inhibitor activity / protein kinase regulator activity / ATP-dependent protein binding / positive regulation of protein localization to cell surface / retina homeostasis / protein folding chaperone complex / Respiratory syncytial virus genome replication / telomerase holoenzyme complex assembly / positive regulation of transforming growth factor beta receptor signaling pathway / Uptake and function of diphtheria toxin / dendritic growth cone / TPR domain binding / Assembly and release of respiratory syncytial virus (RSV) virions / The NLRP3 inflammasome / protein phosphatase activator activity / phototransduction, visible light / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / HSF1 activation / Attenuation phase / chaperone-mediated protein complex assembly / telomere maintenance via telomerase / axonal growth cone / RHOBTB2 GTPase cycle / Purinergic signaling in leishmaniasis infection / : / DNA polymerase binding / heat shock protein binding / supramolecular fiber organization / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / photoreceptor inner segment / protein folding chaperone / peptide binding / cellular response to interleukin-4 / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / placenta development / nitric-oxide synthase regulator activity / positive regulation of cell differentiation / peptidyl-prolyl cis-trans isomerase activity / ATP-dependent protein folding chaperone / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Regulation of actin dynamics for phagocytic cup formation / kinase binding / tau protein binding / histone deacetylase binding / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / disordered domain specific binding / MHC class II protein complex binding / The role of GTSE1 in G2/M progression after G2 checkpoint / unfolded protein binding / melanosome / protein folding / double-stranded RNA binding / regulation of protein localization / cellular response to heat / secretory granule lumen / Estrogen-dependent gene expression / ficolin-1-rich granule lumen / Potential therapeutics for SARS / regulation of cell cycle / protein dimerization activity / protein stabilization / nuclear speck / cadherin binding / neuronal cell body / apoptotic process / ubiquitin protein ligase binding / Neutrophil degranulation / protein kinase binding / negative regulation of apoptotic process / virion attachment to host cell / perinuclear region of cytoplasm / SARS-CoV-2 activates/modulates innate and adaptive immune responses / cell surface / protein homodimerization activity / protein-containing complex / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / AH receptor-interacting protein, N-terminal FKBP-type PPIase / AIP/AIPL1 / 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 ...: / AH receptor-interacting protein, N-terminal FKBP-type PPIase / AIP/AIPL1 / 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 / TPR repeat region circular profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Heat shock protein HSP 90-beta / Aryl-hydrocarbon-interacting protein-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsSrivastava, D. / Artemyev, N.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01 EY-10843 United States
CitationJournal: Structure / Year: 2023
Title: Unique interface and dynamics of the complex of HSP90 with a specialized cochaperone AIPL1.
Authors: Dhiraj Srivastava / Ravi P Yadav / Sneha Singh / Kimberly Boyd / Nikolai O Artemyev /
Abstract: Photoreceptor phosphodiesterase PDE6 is central for visual signal transduction. Maturation of PDE6 depends on a specialized chaperone complex of HSP90 with aryl hydrocarbon receptor-interacting ...Photoreceptor phosphodiesterase PDE6 is central for visual signal transduction. Maturation of PDE6 depends on a specialized chaperone complex of HSP90 with aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1). Disruption of PDE6 maturation underlies a severe form of retina degeneration. Here, we report a 3.9 Å cryoelectron microscopy (cryo-EM) structure of the complex of HSP90 with AIPL1. This structure reveals a unique interaction of the FK506-binding protein (FKBP)-like domain of AIPL1 with HSP90 at its dimer interface. Unusually, the N terminus AIPL1 inserts into the HSP90 lumen in a manner that was observed previously for HSP90 clients. Deletion of the 7 N-terminal residues of AIPL1 decreased its ability to cochaperone PDE6. Multi-body refinement of the cryo-EM data indicated large swing-like movements of AIPL1-FKBP. Modeling the complex of HSP90 with AIPL1 using crosslinking constraints indicated proximity of the mobile tetratricopeptide repeat (TPR) domain with the C-terminal domain of HSP90. Our study establishes a framework for future structural studies of PDE6 maturation.
History
DepositionOct 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 15, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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: Aryl-hydrocarbon-interacting protein-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,1657
Polymers215,1043
Non-polymers1,0614
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Heat shock protein HSP 90-beta / HSP 90 / Heat shock 84 kDa / HSP 84 / HSP84


Mass: 87170.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AB1, HSP90B, HSPC2, HSPCB / Production host: Escherichia coli (E. coli) / Strain (production host): rosetta 2 (DE3) / References: UniProt: P08238
#2: Protein Aryl-hydrocarbon-interacting protein-like 1


Mass: 40763.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aipl1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q924K1
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
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

ComponentName: HSP90B/AIPL1 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.215 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Rosetta 2 (DE3)
Buffer solutionpH: 7.5 / Details: 25 mM HEPES, 200 mM NaCl, 1 mM TCEP, pH 7.5
Buffer component
IDConc.NameBuffer-ID
125 mMHSPES1
2200 mMNaCl1
31 mMTCEP1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS 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: 900 nm
Image recordingAverage exposure time: 0.032 sec. / Electron dose: 1.5 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategory
1cryoSPARCV3.3.2particle selection
7UCSF Chimeramodel fitting
8NAMDmodel fitting
10PHENIX1.2model refinement
11Coot0.9.8.1model refinement
12cryoSPARC3.3.2initial Euler assignment
13cisTEM1final Euler assignment
14cisTEM1classification
15cisTEM13D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 443532
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81152 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00211736
ELECTRON MICROSCOPYf_angle_d0.47115806
ELECTRON MICROSCOPYf_dihedral_angle_d11.3974505
ELECTRON MICROSCOPYf_chiral_restr0.0381763
ELECTRON MICROSCOPYf_plane_restr0.0032012

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