+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9196 | |||||||||
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Title | ADP-bound human mitochondrial Hsp60-Hsp10 half-football complex | |||||||||
Map data | ADP-bound mHsp60-mHsp10 half-football complex | |||||||||
Sample |
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Keywords | Complex / ADP / Half-football / CHAPERONE | |||||||||
Function / homology | Function and homology information coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / lipopolysaccharide receptor complex / apolipoprotein A-I binding / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / 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 / apolipoprotein A-I binding / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / 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 activation / B cell proliferation / DNA replication origin binding / apoptotic mitochondrial changes / positive regulation of interferon-alpha production / chaperone cofactor-dependent protein refolding / apolipoprotein binding / positive regulation of interleukin-10 production / protein maturation / RHOG GTPase cycle / response to unfolded protein / chaperone-mediated protein complex assembly / protein folding chaperone / clathrin-coated pit / isomerase activity / sperm midpiece / response to cold / positive regulation of interleukin-12 production / T cell activation / 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 T cell activation / unfolded protein binding / positive regulation of type II interferon production / p53 binding / double-stranded RNA binding / protein folding / single-stranded DNA binding / protein-folding chaperone binding / protein refolding / mitochondrial inner membrane / protein stabilization / early endosome / 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: 3.82 Å | |||||||||
Authors | Gomez-Llorente Y / Jebara F / Patra M | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structural basis for active single and double ring complexes in human mitochondrial Hsp60-Hsp10 chaperonin. Authors: Yacob Gomez-Llorente / Fady Jebara / Malay Patra / Radhika Malik / Shahar Nisemblat / Orna Chomsky-Hecht / Avital Parnas / Abdussalam Azem / Joel A Hirsch / Iban Ubarretxena-Belandia / Abstract: mHsp60-mHsp10 assists the folding of mitochondrial matrix proteins without the negative ATP binding inter-ring cooperativity of GroEL-GroES. Here we report the crystal structure of an ATP (ADP:BeF- ...mHsp60-mHsp10 assists the folding of mitochondrial matrix proteins without the negative ATP binding inter-ring cooperativity of GroEL-GroES. Here we report the crystal structure of an ATP (ADP:BeF-bound) ground-state mimic double-ring mHsp60-(mHsp10) football complex, and the cryo-EM structures of the ADP-bound successor mHsp60-(mHsp10) complex, and a single-ring mHsp60-mHsp10 half-football. The structures explain the nucleotide dependence of mHsp60 ring formation, and reveal an inter-ring nucleotide symmetry consistent with the absence of negative cooperativity. In the ground-state a two-fold symmetric H-bond and a salt bridge stitch the double-rings together, whereas only the H-bond remains as the equatorial gap increases in an ADP football poised to split into half-footballs. Refolding assays demonstrate obligate single- and double-ring mHsp60 variants are active, and complementation analysis in bacteria shows the single-ring variant is as efficient as wild-type mHsp60. Our work provides a structural basis for active single- and double-ring complexes coexisting in the mHsp60-mHsp10 chaperonin reaction cycle. | |||||||||
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_9196.map.gz | 156.2 MB | EMDB map data format | |
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Header (meta data) | emd-9196-v30.xml emd-9196.xml | 13.1 KB 13.1 KB | Display Display | EMDB header |
Images | emd_9196.png | 79.9 KB | ||
Filedesc metadata | emd-9196.cif.gz | 6.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9196 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9196 | HTTPS FTP |
-Related structure data
Related structure data | 6mrdMC 9195C 6mrcC C: citing same article (ref.) M: atomic model generated by this map |
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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_9196.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | ADP-bound mHsp60-mHsp10 half-football complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 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 : Half-football complex of Hsp60 with Hsp10 bound to ADP and Mg
Entire | Name: Half-football complex of Hsp60 with Hsp10 bound to ADP and Mg |
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Components |
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-Supramolecule #1: Half-football complex of Hsp60 with Hsp10 bound to ADP and Mg
Supramolecule | Name: Half-football complex of Hsp60 with Hsp10 bound to ADP and Mg type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 490 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: ec: 3.6.4.9 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 56.263559 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GSAKDVKFGA DARALMLQGV DLLADAVAVT MGPKGRTVII EQSWGSPKVT KDGVTVAKSI DLKDKYKNIG AKLVQDVANN TNEEAGDGT TTATVLARSI AKEGFEKISK GANPVEIRRG VMLAVDAVIA ELKKQSKPVT TPEEIAQVAT ISANGDKEIG N IISDAMKK ...String: GSAKDVKFGA DARALMLQGV DLLADAVAVT MGPKGRTVII EQSWGSPKVT KDGVTVAKSI DLKDKYKNIG AKLVQDVANN TNEEAGDGT TTATVLARSI AKEGFEKISK GANPVEIRRG VMLAVDAVIA ELKKQSKPVT TPEEIAQVAT ISANGDKEIG N IISDAMKK VGRKGVITVK DGKTLNDELE IIEGMKFDRG YISPYFINTS KGQKCEFQDA YVLLSEKKIS SIQSIVPALE IA NAHRKPL VIIAEDVDGE ALSTLVLNRL KVGLQVVAVK APGFGDNRKN QLKDMAIATG GAVFGEEGLT LNLEDVQPHD LGK VGEVIV TKDDAMLLKG KGDKAQIEKR IQEIIEQLDV TTSEYEKEKL NERLAKLSDG VAVLKVGGTS DVEVNEKKDR VTDA LNATR AAVEEGIVLG GGCALLRCIP ALDSLTPANE DQKIGIEIIK RTLKIPAMTI AKNAGVEGSL IVEKIMQSSS EVGYD AMAG DFVNMVEKGI IDPTKVVRTA LLDAAGVASL LTTAEVVVTE IPKE 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'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 7 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 7 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.7 |
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Grid | Support film - Material: CARBON / Support film - topology: LACEY / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
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: COUNTING / Average exposure time: 10.0 sec. / Average electron dose: 63.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 10972 |