+Open data
-Basic information
Entry | Database: PDB / ID: 8g7j | |||||||||
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Title | mtHsp60 V72I apo | |||||||||
Components | 60 kDa heat shock protein, mitochondrial | |||||||||
Keywords | CHAPERONE / chaperonin / ATPase / foldase | |||||||||
Function / homology | Function and homology information coated vesicle / isotype switching to IgG isotypes / lipopolysaccharide receptor complex / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / apolipoprotein A-I binding / mitochondrial unfolded protein response / migrasome / high-density lipoprotein particle binding / protein import into mitochondrial intermembrane space / positive regulation of T cell mediated immune response to tumor cell ...coated vesicle / isotype switching to IgG isotypes / lipopolysaccharide receptor complex / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / apolipoprotein A-I binding / mitochondrial unfolded protein response / migrasome / high-density lipoprotein particle binding / protein import into mitochondrial intermembrane space / positive regulation of T cell mediated immune response to tumor cell / Mitochondrial protein import / chaperonin ATPase / positive regulation of macrophage activation / cellular response to interleukin-7 / biological process involved in interaction with symbiont / MyD88-dependent toll-like receptor signaling pathway / 'de novo' protein folding / sperm plasma membrane / B cell activation / B cell proliferation / DNA replication origin binding / apoptotic mitochondrial changes / apolipoprotein binding / positive regulation of interleukin-10 production / positive regulation of interferon-alpha production / protein maturation / response to unfolded protein / chaperone-mediated protein complex assembly / clathrin-coated pit / sperm midpiece / Mitochondrial protein degradation / T cell activation / positive regulation of interleukin-12 production / response to cold / isomerase activity / secretory granule / lipopolysaccharide binding / ATP-dependent protein folding chaperone / positive regulation of interleukin-6 production / positive regulation of type II interferon production / activation of cysteine-type endopeptidase activity involved in apoptotic process / double-stranded RNA binding / positive regulation of T cell activation / unfolded protein binding / p53 binding / protein folding / single-stranded DNA binding / protein-folding chaperone binding / protein refolding / mitochondrial inner membrane / early endosome / protein stabilization / mitochondrial matrix / positive regulation of apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / enzyme binding / cell surface / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular space / extracellular exosome / ATP binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Braxton, J.R. / Shao, H. / Tse, E. / Gestwicki, J.E. / Southworth, D.R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: bioRxiv / Year: 2023 Title: Asymmetric apical domain states of mitochondrial Hsp60 coordinate substrate engagement and chaperonin assembly. Authors: Julian R Braxton / Hao Shao / Eric Tse / Jason E Gestwicki / Daniel R Southworth / Abstract: The mitochondrial chaperonin, mtHsp60, promotes the folding of newly imported and transiently misfolded proteins in the mitochondrial matrix, assisted by its co-chaperone mtHsp10. Despite its ...The mitochondrial chaperonin, mtHsp60, promotes the folding of newly imported and transiently misfolded proteins in the mitochondrial matrix, assisted by its co-chaperone mtHsp10. Despite its essential role in mitochondrial proteostasis, structural insights into how this chaperonin binds to clients and progresses through its ATP-dependent reaction cycle are not clear. Here, we determined cryo-electron microscopy (cryo-EM) structures of a hyperstable disease-associated mtHsp60 mutant, V72I, at three stages in this cycle. Unexpectedly, client density is identified in all states, revealing interactions with mtHsp60's apical domains and C-termini that coordinate client positioning in the folding chamber. We further identify a striking asymmetric arrangement of the apical domains in the ATP state, in which an alternating up/down configuration positions interaction surfaces for simultaneous recruitment of mtHsp10 and client retention. Client is then fully encapsulated in mtHsp60/mtHsp10, revealing prominent contacts at two discrete sites that potentially support maturation. These results identify a new role for the apical domains in coordinating client capture and progression through the cycle, and suggest a conserved mechanism of group I chaperonin function. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g7j.cif.gz | 583.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g7j.ent.gz | 491.9 KB | Display | PDB format |
PDBx/mmJSON format | 8g7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/8g7j ftp://data.pdbj.org/pub/pdb/validation_reports/g7/8g7j | HTTPS FTP |
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-Related structure data
Related structure data | 29813MC 8g7kC 8g7lC 8g7mC 8g7nC 8g7oC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 58321.000 Da / Num. of mol.: 7 / Mutation: V72I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSPD1, HSP60 / Production host: Escherichia coli (E. coli) / References: UniProt: P10809, chaperonin ATPase |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Apo Hsp60 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 2.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: Pelco easiGlow, 15 mA / Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Wait time 10 sec, blot time 3 sec, blot force 0 |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 45000 X / Calibrated magnification: 53937 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 66 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 20223 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
Symmetry | Point symmetry: C7 (7 fold cyclic) | |||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 839799 / Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT |