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- EMDB-28333: Cryo-EM structure of human HSP90B in the closed state -

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Basic information

Entry
Database: EMDB / ID: EMD-28333
TitleCryo-EM structure of human HSP90B in the closed state
Map dataCryo-EM structure of human HSP90B in the closed state
Sample
  • Complex: HSP90B dimer in the closed AMPPNP bound state
    • Protein or peptide: Heat shock protein HSP 90-beta
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsHSP90B / AIPL1 / phosphodiesterase 6 / CHAPERONE
Function / homology
Function and homology information


HSP90-CDC37 chaperone complex / receptor ligand inhibitor activity / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / dynein axonemal particle / histone methyltransferase binding / ATP-dependent protein binding / positive regulation of protein localization to cell surface / protein kinase regulator activity ...HSP90-CDC37 chaperone complex / receptor ligand inhibitor activity / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / aryl hydrocarbon receptor complex / dynein axonemal particle / histone methyltransferase binding / ATP-dependent protein binding / positive regulation of protein localization to cell surface / protein kinase regulator activity / protein folding chaperone complex / telomerase holoenzyme complex assembly / Respiratory syncytial virus genome replication / Uptake and function of diphtheria toxin / TPR domain binding / Assembly and release of respiratory syncytial virus (RSV) virions / positive regulation of transforming growth factor beta receptor signaling pathway / dendritic growth cone / The NLRP3 inflammasome / : / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / telomere maintenance via telomerase / HSF1-dependent transactivation / response to unfolded protein / chaperone-mediated protein complex assembly / HSF1 activation / Attenuation phase / RHOBTB2 GTPase cycle / cellular response to interleukin-4 / Purinergic signaling in leishmaniasis infection / axonal growth cone / DNA polymerase binding / supramolecular fiber organization / chaperone-mediated protein folding / heat shock protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / protein folding chaperone / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / nitric-oxide synthase regulator activity / ESR-mediated signaling / positive regulation of cell differentiation / ATP-dependent protein folding chaperone / peptide binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / placenta development / tau protein binding / kinase binding / Regulation of actin dynamics for phagocytic cup formation / histone deacetylase binding / Chaperone Mediated Autophagy / The role of GTSE1 in G2/M progression after G2 checkpoint / disordered domain specific binding / positive regulation of nitric oxide biosynthetic process / double-stranded RNA binding / unfolded protein binding / melanosome / protein folding / MHC class II protein complex 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 / protein dimerization activity / regulation of cell cycle / protein stabilization / cadherin binding / neuronal cell body / ubiquitin protein ligase binding / Neutrophil degranulation / negative regulation of apoptotic process / virion attachment to host cell / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSrivastava D / Artemyev NO
Funding support United States, 1 items
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, 2022-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28333.png

Downloads & links

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Map

FileDownload / File: emd_28333.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of human HSP90B in the closed state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 200 pix.
= 249.2 Å		1.25 Å/pix.
x 200 pix.
= 249.2 Å		1.25 Å/pix.
x 200 pix.
= 249.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.246 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.2
Minimum - Maximum-11.448881999999999 - 31.791640999999998
Average (Standard dev.)0.0010798957 (±0.96887445)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 249.20001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28333_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1

Fileemd_28333_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_28333_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : HSP90B dimer in the closed AMPPNP bound state

EntireName: HSP90B dimer in the closed AMPPNP bound state
Components
  • Complex: HSP90B dimer in the closed AMPPNP bound state
    • Protein or peptide: Heat shock protein HSP 90-beta
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: HSP90B dimer in the closed AMPPNP bound state

SupramoleculeName: HSP90B dimer in the closed AMPPNP bound state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 174 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 / Details: HSP90B / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.170227 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHHHHHHDYD IPTTGYPYDV PDYAENLYFQ GASPEEVHHG EEEVETFAFQ AEIAQLMSLI INTFYSNKEI FLRELISNAS DALDKIRYE SLTDPSKLDS GKELKIDIIP NPQERTLTLV DTGIGMTKAD LINNLGTIAK SGTKAFMEAL QAGADISMIG Q FGVGFYSA ...String:
MHHHHHHDYD IPTTGYPYDV PDYAENLYFQ GASPEEVHHG 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 EKEEEDKDDE 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 IDEDEVAAEE PNAAVPDEIP PLEGDEDASR MEEVD

UniProtKB: Heat shock protein HSP 90-beta

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Macromolecule #2: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
25.0 mMHSPES
200.0 mMNaCl
1.0 mMTCEP

Details: 25 mM HEPES, 200 mM NaCl, 1 mM TCEP, pH 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 0.032 sec. / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 116639
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0) / Details: masked FSC resolution / Number images used: 440225
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cisTEM (ver. 1.0)
Final 3D classificationSoftware - Name: cisTEM (ver. 1.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8eob:
Cryo-EM structure of human HSP90B in the closed state

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