+Open data
-Basic information
Entry | Database: PDB / ID: 8u39 | ||||||
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Title | Structure of Human Mitochondrial Chaperonin V72I mutant | ||||||
Components | 60 kDa heat shock protein, mitochondrial | ||||||
Keywords | CHAPERONE / chaperonin / human mitochondrial mHsp60 / hereditary spastic paraplegia SPG13 / cryo-EM / molecular dynamic simulation | ||||||
Function / homology | Function and homology information coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / apolipoprotein A-I binding / lipopolysaccharide receptor complex / protein import into mitochondrial intermembrane space / migrasome / high-density lipoprotein particle binding / positive regulation of T cell mediated immune response to tumor cell ...coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / apolipoprotein A-I binding / lipopolysaccharide receptor complex / protein import into mitochondrial intermembrane space / migrasome / high-density lipoprotein particle binding / 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 / MyD88-dependent toll-like receptor signaling pathway / biological process involved in interaction with symbiont / 'de novo' protein folding / sperm plasma membrane / B cell proliferation / B cell activation / apolipoprotein binding / DNA replication origin binding / positive regulation of interferon-alpha production / apoptotic mitochondrial changes / protein maturation / positive regulation of interleukin-10 production / response to unfolded protein / chaperone-mediated protein complex assembly / clathrin-coated pit / sperm midpiece / positive regulation of interleukin-12 production / Mitochondrial protein degradation / response to cold / T cell activation / secretory granule / isomerase activity / lipopolysaccharide binding / ATP-dependent protein folding chaperone / : / positive regulation of interleukin-6 production / positive regulation of type II interferon production / 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 | Chen, L. / Wang, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2024 Title: Cryo-EM structure and molecular dynamic simulations explain the enhanced stability and ATP activity of the pathological chaperonin mutant. Authors: Aiza Syed / Jihang Zhai / Baolin Guo / Yuan Zhao / Joseph Che-Yen Wang / Lingling Chen / Abstract: Chaperonins Hsp60s are required for cellular vitality by assisting protein folding in an ATP-dependent mechanism. Although conserved, the human mitochondrial mHsp60 exhibits molecular characteristics ...Chaperonins Hsp60s are required for cellular vitality by assisting protein folding in an ATP-dependent mechanism. Although conserved, the human mitochondrial mHsp60 exhibits molecular characteristics distinct from the E. coli GroEL, with different conformational assembly and higher subunit association dynamics, suggesting a different mechanism. We previously found that the pathological mutant mHsp60 exhibits enhanced subunit association stability and ATPase activity. To provide structural explanations for the V72I mutational effects, here we determined a cryo-EM structure of mHsp60. Our structural analysis combined with molecular dynamic simulations showed mHsp60 with increased inter-subunit interface, binding free energy, and dissociation force, all contributing to its enhanced subunit association stability. The gate to the nucleotide-binding (NB) site in mHsp60 mimicked the open conformation in the nucleotide-bound state with an additional open channel leading to the NB site, both promoting the mutant's ATPase activity. Our studies highlight the importance of mHsp60's characteristics in its biological function. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8u39.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8u39.ent.gz | 954.8 KB | Display | PDB format |
PDBx/mmJSON format | 8u39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8u39_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8u39_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8u39_validation.xml.gz | 110.4 KB | Display | |
Data in CIF | 8u39_validation.cif.gz | 163.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/8u39 ftp://data.pdbj.org/pub/pdb/validation_reports/u3/8u39 | HTTPS FTP |
-Related structure data
Related structure data | 41854MC 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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-Components
#1: Protein | Mass: 55875.164 Da / Num. of mol.: 7 / Fragment: UNP residues 27-550 / Mutation: V72I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSPD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P10809 |
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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: Human Mitochondrial Chaperonin V72I Mutant / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 60 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 7.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 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 | Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-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: 532348 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7L7S Accession code: 7L7S / Source name: PDB / Type: experimental model |