+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29818 | |||||||||
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Title | ATP- and mtHsp10-bound mtHsp60 V72I focus | |||||||||
Map data | ||||||||||
Sample |
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Keywords | chaperonin / ATPase / foldase / CHAPERONE | |||||||||
Function / homology | Function and homology information coated vesicle / isotype switching to IgG isotypes / lipopolysaccharide receptor complex / apolipoprotein A-I binding / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / migrasome / high-density lipoprotein particle binding / positive regulation of T cell mediated immune response to tumor cell / mitochondrial unfolded protein response / chaperonin ATPase ...coated vesicle / isotype switching to IgG isotypes / lipopolysaccharide receptor complex / apolipoprotein A-I binding / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / migrasome / high-density lipoprotein particle binding / positive regulation of T cell mediated immune response to tumor cell / mitochondrial unfolded protein response / chaperonin ATPase / Mitochondrial protein import / protein import into mitochondrial intermembrane space / 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 / chaperone cofactor-dependent protein refolding / positive regulation of interleukin-10 production / protein maturation / RHOG GTPase cycle / response to unfolded protein / chaperone-mediated protein complex assembly / positive regulation of interferon-alpha production / Mitochondrial protein degradation / protein folding chaperone / clathrin-coated pit / sperm midpiece / isomerase activity / T cell activation / positive regulation of interleukin-12 production / response to cold / secretory granule / lipopolysaccharide binding / ATP-dependent protein folding chaperone / osteoblast differentiation / positive regulation of interleukin-6 production / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of type II interferon production / double-stranded RNA binding / unfolded protein binding / p53 binding / positive regulation of T cell activation / 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 / extracellular space / RNA binding / extracellular exosome / ATP binding / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Braxton JR / Shao H / Tse E / Gestwicki JE / Southworth DR | |||||||||
Funding support | United States, 2 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29818.map.gz | 328.5 MB | EMDB map data format | |
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Header (meta data) | emd-29818-v30.xml emd-29818.xml | 21.3 KB 21.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29818_fsc.xml emd_29818_fsc_2.xml | 15 KB 15.1 KB | Display Display | FSC data file |
Images | emd_29818.png | 182.4 KB | ||
Filedesc metadata | emd-29818.cif.gz | 6.1 KB | ||
Others | emd_29818_additional_1.map.gz emd_29818_half_map_1.map.gz emd_29818_half_map_2.map.gz | 173.6 MB 322.3 MB 322.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29818 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29818 | HTTPS FTP |
-Related structure data
Related structure data | 8g7oMC 8g7jC 8g7kC 8g7lC 8g7mC 8g7nC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_29818.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.927 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Unsharpened map
File | emd_29818_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29818_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_29818_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ATP- and mtHsp10-bound mtHsp60
Entire | Name: ATP- and mtHsp10-bound mtHsp60 |
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Components |
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-Supramolecule #1: ATP- and mtHsp10-bound mtHsp60
Supramolecule | Name: ATP- and mtHsp10-bound mtHsp60 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-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: 56.204535 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: AAKDVKFGAD ARALMLQGVD LLADAVAVTM GPKGRTVIIE QSWGSPKVTK DGVTVAKSID LKDKYKNIGA KLIQDVANNT NEEAGDGTT TATVLARSIA KEGFEKISKG ANPVEIRRGV MLAVDAVIAE LKKQSKPVTT PEEIAQVATI SANGDKEIGN I ISDAMKKV ...String: AAKDVKFGAD ARALMLQGVD LLADAVAVTM GPKGRTVIIE QSWGSPKVTK DGVTVAKSID LKDKYKNIGA KLIQDVANNT NEEAGDGTT TATVLARSIA KEGFEKISKG ANPVEIRRGV MLAVDAVIAE LKKQSKPVTT PEEIAQVATI SANGDKEIGN I ISDAMKKV GRKGVITVKD GKTLNDELEI IEGMKFDRGY ISPYFINTSK GQKCEFQDAY VLLSEKKISS IQSIVPALEI AN AHRKPLV IIAEDVDGEA LSTLVLNRLK VGLQVVAVKA PGFGDNRKNQ LKDMAIATGG AVFGEEGLTL NLEDVQPHDL GKV GEVIVT KDDAMLLKGK GDKAQIEKRI QEIIEQLDVT TSEYEKEKLN ERLAKLSDGV AVLKVGGTSD VEVNEKKDRV TDAL NATRA AVEEGIVLGG GCALLRCIPA LDSLTPANED QKIGIEIIKR TLKIPAMTIA KNAGVEGSLI VEKIMQSSSE VGYDA MAGD FVNMVEKGII DPTKVVRTAL LDAAGVASLL TTAEVVVTEI PKE UniProtKB: 60 kDa heat shock protein, mitochondrial |
-Macromolecule #2: 10 kDa heat shock protein, mitochondrial
Macromolecule | Name: 10 kDa heat shock protein, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 10.7444 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GQAFRKFLPL FDRVLVERSA AETVTKGGIM LPEKSQGKVL QATVVAVGSG SKGKGGEIQP VSVKVGDKVL LPEYGGTKVV LDDKDYFLF RDGDILGKYV D UniProtKB: 10 kDa heat shock protein, mitochondrial |
-Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 7 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4.8 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.03 kPa / Details: Pelco easiGlow, 15 mA |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: Wait time 10 sec, blot time 3 sec, blot force 0. |
-Electron microscopy
Microscope | TFS GLACIOS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 53937 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 45000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 2 / Number real images: 7460 / Average exposure time: 10.0 sec. / Average electron dose: 66.0 e/Å2 |
-Image processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | PDB-8g7o: |