+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29813 | |||||||||
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Title | mtHsp60 V72I apo | |||||||||
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 / 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 / T cell activation / positive regulation of interleukin-12 production / response to cold / isomerase activity / secretory granule / Mitochondrial protein degradation / lipopolysaccharide binding / ATP-dependent protein folding chaperone / p53 binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / protein folding / single-stranded DNA binding / protein-folding chaperone binding / protein refolding / early endosome / protein stabilization / mitochondrial inner membrane / 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 / cytoplasm / cytosol 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_29813.map.gz | 156.6 MB | EMDB map data format | |
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Header (meta data) | emd-29813-v30.xml emd-29813.xml | 19.8 KB 19.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29813_fsc.xml emd_29813_fsc_2.xml | 11.7 KB 11.8 KB | Display Display | FSC data file |
Images | emd_29813.png | 174.3 KB | ||
Filedesc metadata | emd-29813.cif.gz | 5.9 KB | ||
Others | emd_29813_additional_1.map.gz emd_29813_half_map_1.map.gz emd_29813_half_map_2.map.gz | 80.8 MB 154 MB 154 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29813 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29813 | HTTPS FTP |
-Validation report
Summary document | emd_29813_validation.pdf.gz | 826.5 KB | Display | EMDB validaton report |
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Full document | emd_29813_full_validation.pdf.gz | 826.1 KB | Display | |
Data in XML | emd_29813_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | emd_29813_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29813 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29813 | HTTPS FTP |
-Related structure data
Related structure data | 8g7jMC 8g7kC 8g7lC 8g7mC 8g7nC 8g7oC 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_29813.map.gz / Format: CCP4 / Size: 166.4 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_29813_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_29813_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29813_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Apo Hsp60
Entire | Name: Apo Hsp60 |
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Components |
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-Supramolecule #1: Apo Hsp60
Supramolecule | Name: Apo Hsp60 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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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: 58.321 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SNAAKDVKFG ADARALMLQG VDLLADAVAV TMGPKGRTVI IEQSWGSPKV TKDGVTVAKS IDLKDKYKNI GAKLIQDVAN NTNEEAGDG TTTATVLARS IAKEGFEKIS KGANPVEIRR GVMLAVDAVI AELKKQSKPV TTPEEIAQVA TISANGDKEI G NIISDAMK ...String: SNAAKDVKFG ADARALMLQG VDLLADAVAV TMGPKGRTVI IEQSWGSPKV TKDGVTVAKS IDLKDKYKNI GAKLIQDVAN NTNEEAGDG TTTATVLARS IAKEGFEKIS KGANPVEIRR GVMLAVDAVI AELKKQSKPV TTPEEIAQVA TISANGDKEI G NIISDAMK KVGRKGVITV KDGKTLNDEL EIIEGMKFDR GYISPYFINT SKGQKCEFQD AYVLLSEKKI SSIQSIVPAL EI ANAHRKP LVIIAEDVDG EALSTLVLNR LKVGLQVVAV KAPGFGDNRK NQLKDMAIAT GGAVFGEEGL TLNLEDVQPH DLG KVGEVI VTKDDAMLLK GKGDKAQIEK RIQEIIEQLD VTTSEYEKEK LNERLAKLSD GVAVLKVGGT SDVEVNEKKD RVTD ALNAT RAAVEEGIVL GGGCALLRCI PALDSLTPAN EDQKIGIEII KRTLKIPAMT IAKNAGVEGS LIVEKIMQSS SEVGY DAMA GDFVNMVEKG IIDPTKVVRT ALLDAAGVAS LLTTAEVVVT EIPKEEKDPG MGAMGGMGGG MGGGMF 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 | 2.4 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / 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: 277 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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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 2 / Number real images: 20223 / Average exposure time: 10.0 sec. / Average electron dose: 66.0 e/Å2 |
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 FIELD / 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 processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | PDB-8g7j: |