+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23217 | |||||||||
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Title | Human mitochondrial chaperonin mHsp60 | |||||||||
Map data | Cryo-EM structure of mHsp60 | |||||||||
Sample |
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Keywords | mHsp60 / GroEL / chaperonin / CHAPERONE / ISOMERASE | |||||||||
Function / homology | Function and homology information coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / lipopolysaccharide receptor complex / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / apolipoprotein A-I binding / 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 / lipopolysaccharide receptor complex / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / apolipoprotein A-I binding / 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 / biological process involved in interaction with symbiont / MyD88-dependent toll-like receptor signaling pathway / 'de novo' protein folding / sperm plasma membrane / B cell proliferation / B cell activation / positive regulation of interferon-alpha production / apoptotic mitochondrial changes / DNA replication origin binding / apolipoprotein binding / positive regulation of interleukin-10 production / protein maturation / response to unfolded protein / chaperone-mediated protein complex assembly / clathrin-coated pit / sperm midpiece / Mitochondrial protein degradation / positive regulation of interleukin-12 production / response to cold / T cell activation / secretory granule / isomerase activity / lipopolysaccharide binding / ATP-dependent protein folding chaperone / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of interleukin-6 production / positive regulation of type II interferon production / positive regulation of T cell activation / double-stranded RNA binding / unfolded protein binding / p53 binding / protein folding / protein-folding chaperone binding / single-stranded DNA 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 | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Chen L / Wang JCY | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Sci Rep / Year: 2021 Title: Structural basis for the structural dynamics of human mitochondrial chaperonin mHsp60. Authors: Joseph Che-Yen Wang / Lingling Chen / Abstract: Human mitochondrial chaperonin mHsp60 is essential for mitochondrial function by assisting folding of mitochondrial proteins. Unlike the double-ring bacterial GroEL, mHsp60 exists as a heptameric ...Human mitochondrial chaperonin mHsp60 is essential for mitochondrial function by assisting folding of mitochondrial proteins. Unlike the double-ring bacterial GroEL, mHsp60 exists as a heptameric ring that is unstable and dissociates to subunits. The structural dynamics has been implicated for a unique mechanism of mHsp60. We purified active heptameric mHsp60, and determined a cryo-EM structure of mHsp60 heptamer at 3.4 Å. Of the three domains, the equatorial domains contribute most to the inter-subunit interactions, which include a four-stranded β sheet. Our structural comparison with GroEL shows that mHsp60 contains several unique sequences that directly decrease the sidechain interactions around the β sheet and indirectly shorten β strands by disengaging the backbones of the flanking residues from hydrogen bonding in the β strand conformation. The decreased inter-subunit interactions result in a small inter-subunit interface in mHsp60 compared to GroEL, providing a structural basis for the dynamics of mHsp60 subunit association. Importantly, the unique sequences are conserved among higher eukaryotic mitochondrial chaperonins, suggesting the importance of structural dynamics for eukaryotic chaperonins. Our structural comparison with the single-ring mHsp60-mHsp10 shows that upon mHsp10 binding the shortened inter-subunit β sheet is restored and the overall inter-subunit interface of mHsp60 increases drastically. Our structural basis for the mHsp10 induced stabilization of mHsp60 subunit interaction is consistent with the literature that mHsp10 stabilizes mHsp60 quaternary structure. Together, our studies provide structural bases for structural dynamics of the mHsp60 heptamer and for the stabilizing effect of mHsp10 on mHsp60 subunit association. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23217.map.gz | 117 MB | EMDB map data format | |
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Header (meta data) | emd-23217-v30.xml emd-23217.xml | 18 KB 18 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23217_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_23217.png | 66.9 KB | ||
Filedesc metadata | emd-23217.cif.gz | 5.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23217 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23217 | HTTPS FTP |
-Validation report
Summary document | emd_23217_validation.pdf.gz | 584.7 KB | Display | EMDB validaton report |
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Full document | emd_23217_full_validation.pdf.gz | 584.3 KB | Display | |
Data in XML | emd_23217_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_23217_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23217 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23217 | HTTPS FTP |
-Related structure data
Related structure data | 7l7sMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23217.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of mHsp60 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Human mitochondrial chaperonin mHsp60 in a heptameric ring confor...
Entire | Name: Human mitochondrial chaperonin mHsp60 in a heptameric ring conformation |
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Components |
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-Supramolecule #1: Human mitochondrial chaperonin mHsp60 in a heptameric ring confor...
Supramolecule | Name: Human mitochondrial chaperonin mHsp60 in a heptameric ring conformation type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Human mitochondrial chaperonin mHsp60 in a heptameric ring conformation |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 60 KDa |
-Macromolecule #1: 60 kDa heat shock protein, mitochondrial
Macromolecule | Name: 60 kDa heat shock protein, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO / EC number: chaperonin ATPase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 55.861137 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: AKDVKFGADA RALMLQGVDL LADAVAVTMG PKGRTVIIEQ SWGSPKVTKD GVTVAKSIDL KDKYKNIGAK LVQDVANNTN EEAGDGTTT ATVLARSIAK EGFEKISKGA NPVEIRRGVM LAVDAVIAEL KKQSKPVTTP EEIAQVATIS ANGDKEIGNI I SDAMKKVG ...String: AKDVKFGADA RALMLQGVDL LADAVAVTMG PKGRTVIIEQ SWGSPKVTKD GVTVAKSIDL KDKYKNIGAK LVQDVANNTN EEAGDGTTT ATVLARSIAK EGFEKISKGA NPVEIRRGVM LAVDAVIAEL KKQSKPVTTP EEIAQVATIS ANGDKEIGNI I SDAMKKVG RKGVITVKDG KTLNDELEII EGMKFDRGYI SPYFINTSKG QKCEFQDAYV LLSEKKISSI QSIVPALEIA NA HRKPLVI IAEDVDGEAL STLVLNRLKV GLQVVAVKAP GFGDNRKNQL KDMAIATGGA VFGEEGLTLN LEDVQPHDLG KVG EVIVTK DDAMLLKGKG DKAQIEKRIQ EIIEQLDVTT SEYEKEKLNE RLAKLSDGVA VLKVGGTSDV EVNEKKDRVT DALN ATRAA VEEGIVLGGG CALLRCIPAL DSLTPANEDQ KIGIEIIKRT LKIPAMTIAK NAGVEGSLIV EKIMQSSSEV GYDAM AGDF VNMVEKGIID PTKVVRTALL DAAGVASLLT TAEVVVTEIP UniProtKB: 60 kDa heat shock protein, mitochondrial |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 9 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: GOLD / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: HOLEY | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV | ||||||||||||||||||
Details | The sample is monodisperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 30 eV |
Image recording | #0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #0 - Number grids imaged: 1 / #0 - Average electron dose: 44.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Number grids imaged: 3 / #1 - Average electron dose: 53.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing #1
+Image processing #2
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT | ||||||||||||||||
Output model | PDB-7l7s: |